diff --git a/scripts/generate_trimmed_msas.ps1 b/scripts/generate_trimmed_msas.ps1 index be61da6f..70e5945f 100644 --- a/scripts/generate_trimmed_msas.ps1 +++ b/scripts/generate_trimmed_msas.ps1 @@ -8,507 +8,507 @@ New-Item -ItemType Directory -Path "test_msas\nogaps" New-Item -ItemType Directory -Path "test_msas\noallgaps" # Run trimal commands -.\trimal.exe -in dataset\example.004.AA.fasta -gappyout > test_msas\gappyout\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -strict > test_msas\strict\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -strictplus > test_msas\strictplus\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -automated1 > test_msas\automated1\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -nogaps > test_msas\nogaps\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -noallgaps > test_msas\noallgaps\example.004.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -gappyout > test_msas\gappyout\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -strict > test_msas\strict\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -strictplus > test_msas\strictplus\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -automated1 > test_msas\automated1\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -nogaps > test_msas\nogaps\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -noallgaps > test_msas\noallgaps\example.005.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -gappyout > test_msas\gappyout\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -strict > test_msas\strict\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -strictplus > test_msas\strictplus\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -automated1 > test_msas\automated1\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -nogaps > test_msas\nogaps\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -noallgaps > test_msas\noallgaps\example.007.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -gappyout > test_msas\gappyout\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -strict > test_msas\strict\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -strictplus > test_msas\strictplus\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -automated1 > test_msas\automated1\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -nogaps > test_msas\nogaps\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -noallgaps > test_msas\noallgaps\example.009.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -gappyout > test_msas\gappyout\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -strict > test_msas\strict\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -strictplus > test_msas\strictplus\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -automated1 > test_msas\automated1\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -nogaps > test_msas\nogaps\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -noallgaps > test_msas\noallgaps\example.010.AA.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -gappyout > test_msas\gappyout\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strict > test_msas\strict\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strictplus > test_msas\strictplus\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -automated1 > test_msas\automated1\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -nogaps > test_msas\nogaps\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -noallgaps > test_msas\noallgaps\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas\gappyout\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strict > test_msas\strict\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas\strictplus\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas\automated1\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas\nogaps\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas\noallgaps\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas\gappyout\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas\strict\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas\strictplus\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas\automated1\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas\nogaps\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas\noallgaps\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas\gappyout\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas\strict\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas\strictplus\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas\automated1\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas\nogaps\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas\noallgaps\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas\gappyout\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas\strict\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas\strictplus\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas\automated1\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas\nogaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas\noallgaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas\gappyout\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas\strict\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas\strictplus\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas\automated1\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas\nogaps\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas\noallgaps\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas\gappyout\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas\strict\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas\strictplus\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas\automated1\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas\nogaps\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas\noallgaps\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas\gappyout\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas\strict\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas\strictplus\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas\automated1\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas\nogaps\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas\noallgaps\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas\gappyout\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas\strict\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas\strictplus\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas\automated1\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas\nogaps\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas\noallgaps\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas\gappyout\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas\strict\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas\strictplus\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas\automated1\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas\nogaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas\noallgaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas\gappyout\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas\strict\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas\strictplus\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas\automated1\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas\nogaps\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas\noallgaps\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas\gappyout\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas\strict\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas\strictplus\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas\automated1\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas\nogaps\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas\noallgaps\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas\gappyout\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas\strict\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas\strictplus\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas\automated1\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas\nogaps\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas\noallgaps\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas\gappyout\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas\strict\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas\strictplus\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas\automated1\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas\nogaps\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas\noallgaps\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas\gappyout\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas\strict\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas\strictplus\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas\automated1\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas\nogaps\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas\noallgaps\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas\gappyout\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas\strict\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas\strictplus\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas\automated1\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas\nogaps\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas\noallgaps\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas\gappyout\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas\strict\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas\strictplus\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas\automated1\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas\nogaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas\noallgaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas\gappyout\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas\strict\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas\strictplus\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas\automated1\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas\nogaps\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas\noallgaps\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas\gappyout\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas\strict\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas\strictplus\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas\automated1\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas\nogaps\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas\noallgaps\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas\gappyout\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas\strict\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas\strictplus\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas\automated1\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas\nogaps\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas\noallgaps\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas\gappyout\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas\strict\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas\strictplus\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas\automated1\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas\nogaps\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas\noallgaps\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas\gappyout\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas\strict\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas\strictplus\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas\automated1\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas\nogaps\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas\noallgaps\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas\gappyout\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas\strict\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas\strictplus\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas\automated1\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas\nogaps\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas\noallgaps\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas\gappyout\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas\strict\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas\strictplus\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas\automated1\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas\nogaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas\noallgaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas\gappyout\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas\strict\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas\strictplus\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas\automated1\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas\nogaps\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas\noallgaps\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas\gappyout\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas\strict\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas\strictplus\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas\automated1\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas\nogaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas\noallgaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas\gappyout\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas\strict\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas\strictplus\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas\automated1\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas\nogaps\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas\noallgaps\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas\gappyout\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas\strict\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas\strictplus\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas\automated1\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas\nogaps\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas\noallgaps\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas\gappyout\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas\strict\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas\strictplus\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas\automated1\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas\nogaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas\noallgaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas\gappyout\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas\strict\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas\strictplus\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas\automated1\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas\nogaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas\noallgaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas\gappyout\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas\strict\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas\strictplus\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas\automated1\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas\nogaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas\noallgaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas\gappyout\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas\strict\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas\strictplus\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas\automated1\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas\nogaps\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas\noallgaps\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas\gappyout\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas\strict\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas\strictplus\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas\automated1\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas\nogaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas\noallgaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas\gappyout\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas\strict\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas\strictplus\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas\automated1\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas\nogaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas\noallgaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas\gappyout\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas\strict\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas\strictplus\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas\automated1\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas\nogaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas\noallgaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas\gappyout\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas\strict\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas\strictplus\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas\automated1\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas\nogaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas\noallgaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas\gappyout\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas\strict\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas\strictplus\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas\automated1\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas\nogaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas\noallgaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas\gappyout\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas\strict\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas\strictplus\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas\automated1\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas\nogaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas\noallgaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas\gappyout\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas\strict\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas\strictplus\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas\automated1\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas\nogaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas\noallgaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas\gappyout\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas\strict\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas\strictplus\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas\automated1\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas\nogaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas\noallgaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas\gappyout\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas\strict\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas\strictplus\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas\automated1\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas\nogaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas\noallgaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas\gappyout\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas\strict\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas\strictplus\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas\automated1\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas\nogaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas\noallgaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas\gappyout\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas\strict\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas\strictplus\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas\automated1\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas\nogaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas\noallgaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas\gappyout\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas\strict\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas\strictplus\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas\automated1\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas\nogaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas\noallgaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas\gappyout\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas\strict\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas\strictplus\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas\automated1\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas\nogaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas\noallgaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas\gappyout\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas\strict\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas\strictplus\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas\automated1\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas\nogaps\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas\noallgaps\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas\gappyout\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas\strict\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas\strictplus\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas\automated1\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas\nogaps\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas\noallgaps\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas\gappyout\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas\strict\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas\strictplus\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas\automated1\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas\nogaps\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas\noallgaps\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas\gappyout\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas\strict\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas\strictplus\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas\automated1\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas\nogaps\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas\noallgaps\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas\gappyout\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas\strict\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas\strictplus\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas\automated1\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas\nogaps\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas\noallgaps\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas\gappyout\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas\strict\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas\strictplus\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas\automated1\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas\nogaps\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas\noallgaps\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas\gappyout\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas\strict\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas\strictplus\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas\automated1\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas\nogaps\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas\noallgaps\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas\gappyout\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas\strict\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas\strictplus\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas\automated1\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas\nogaps\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas\noallgaps\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas\gappyout\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas\strict\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas\strictplus\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas\automated1\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas\nogaps\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas\noallgaps\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas\gappyout\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas\strict\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas\strictplus\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas\automated1\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas\nogaps\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas\noallgaps\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas\gappyout\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas\strict\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas\strictplus\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas\automated1\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas\nogaps\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas\noallgaps\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas\gappyout\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas\strict\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas\strictplus\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas\automated1\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas\nogaps\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas\noallgaps\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas\gappyout\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas\strict\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas\strictplus\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas\automated1\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas\nogaps\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas\noallgaps\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas\gappyout\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas\strict\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas\strictplus\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas\automated1\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas\nogaps\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas\noallgaps\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas\gappyout\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas\strict\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas\strictplus\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas\automated1\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas\nogaps\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas\noallgaps\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas\gappyout\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas\strict\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas\strictplus\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas\automated1\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas\nogaps\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas\noallgaps\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas\gappyout\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas\strict\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas\strictplus\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas\automated1\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas\nogaps\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas\noallgaps\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas\gappyout\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas\strict\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas\strictplus\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas\automated1\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas\nogaps\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas\noallgaps\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas\gappyout\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas\strict\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas\strictplus\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas\automated1\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas\nogaps\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas\noallgaps\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas\gappyout\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas\strict\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas\strictplus\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas\automated1\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas\nogaps\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas\noallgaps\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas\gappyout\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas\strict\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas\strictplus\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas\automated1\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas\nogaps\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas\noallgaps\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas\gappyout\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas\strict\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas\strictplus\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas\automated1\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas\nogaps\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas\noallgaps\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas\gappyout\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas\strict\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas\strictplus\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas\automated1\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas\nogaps\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas\noallgaps\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas\gappyout\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas\strict\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas\strictplus\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas\automated1\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas\nogaps\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas\noallgaps\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas\gappyout\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas\strict\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas\strictplus\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas\automated1\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas\nogaps\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas\noallgaps\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas\gappyout\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas\strict\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas\strictplus\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas\automated1\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas\nogaps\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas\noallgaps\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas\gappyout\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas\strict\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas\strictplus\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas\automated1\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas\nogaps\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas\noallgaps\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas\gappyout\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas\strict\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas\strictplus\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas\automated1\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas\nogaps\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas\noallgaps\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas\gappyout\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas\strict\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas\strictplus\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas\automated1\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas\nogaps\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas\noallgaps\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas\gappyout\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas\strict\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas\strictplus\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas\automated1\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas\nogaps\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas\noallgaps\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas\gappyout\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas\strict\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas\strictplus\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas\automated1\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas\nogaps\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas\noallgaps\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas\gappyout\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas\strict\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas\strictplus\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas\automated1\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas\nogaps\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas\noallgaps\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas\gappyout\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas\strict\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas\strictplus\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas\automated1\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas\nogaps\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas\noallgaps\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas\gappyout\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas\strict\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas\strictplus\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas\automated1\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas\nogaps\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas\noallgaps\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -gappyout > test_msas\gappyout\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -strict > test_msas\strict\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -strictplus > test_msas\strictplus\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -automated1 > test_msas\automated1\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -nogaps > test_msas\nogaps\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -noallgaps > test_msas\noallgaps\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -gappyout > test_msas\gappyout\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -strict > test_msas\strict\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -strictplus > test_msas\strictplus\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -automated1 > test_msas\automated1\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -nogaps > test_msas\nogaps\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -noallgaps > test_msas\noallgaps\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -gappyout > test_msas\gappyout\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -strict > test_msas\strict\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -strictplus > test_msas\strictplus\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -automated1 > test_msas\automated1\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -nogaps > test_msas\nogaps\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -noallgaps > test_msas\noallgaps\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -gappyout > test_msas\gappyout\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -strict > test_msas\strict\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -strictplus > test_msas\strictplus\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -automated1 > test_msas\automated1\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -nogaps > test_msas\nogaps\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -noallgaps > test_msas\noallgaps\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -gappyout > test_msas\gappyout\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -strict > test_msas\strict\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -strictplus > test_msas\strictplus\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -automated1 > test_msas\automated1\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -nogaps > test_msas\nogaps\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -noallgaps > test_msas\noallgaps\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -gappyout > test_msas\gappyout\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strict > test_msas\strict\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strictplus > test_msas\strictplus\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -automated1 > test_msas\automated1\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -nogaps > test_msas\nogaps\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -noallgaps > test_msas\noallgaps\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas\gappyout\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strict > test_msas\strict\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas\strictplus\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas\automated1\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas\nogaps\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas\noallgaps\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas\gappyout\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas\strict\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas\strictplus\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas\automated1\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas\nogaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas\noallgaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas\gappyout\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas\strict\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas\strictplus\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas\automated1\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas\nogaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas\noallgaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas\gappyout\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas\strict\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas\strictplus\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas\automated1\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas\nogaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas\noallgaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas\gappyout\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas\strict\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas\strictplus\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas\automated1\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas\nogaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas\noallgaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas\gappyout\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas\strict\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas\strictplus\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas\automated1\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas\nogaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas\noallgaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas\gappyout\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas\strict\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas\strictplus\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas\automated1\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas\nogaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas\noallgaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas\gappyout\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas\strict\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas\strictplus\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas\automated1\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas\nogaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas\noallgaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas\gappyout\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas\strict\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas\strictplus\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas\automated1\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas\nogaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas\noallgaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas\gappyout\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas\strict\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas\strictplus\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas\automated1\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas\nogaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas\noallgaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas\gappyout\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas\strict\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas\strictplus\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas\automated1\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas\nogaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas\noallgaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas\gappyout\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas\strict\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas\strictplus\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas\automated1\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas\nogaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas\noallgaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas\gappyout\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas\strict\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas\strictplus\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas\automated1\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas\nogaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas\noallgaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas\gappyout\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas\strict\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas\strictplus\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas\automated1\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas\nogaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas\noallgaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas\gappyout\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas\strict\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas\strictplus\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas\automated1\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas\nogaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas\noallgaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas\gappyout\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas\strict\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas\strictplus\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas\automated1\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas\nogaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas\noallgaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas\gappyout\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas\strict\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas\strictplus\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas\automated1\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas\nogaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas\noallgaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas\gappyout\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas\strict\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas\strictplus\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas\automated1\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas\nogaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas\noallgaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas\gappyout\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas\strict\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas\strictplus\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas\automated1\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas\nogaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas\noallgaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas\gappyout\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas\strict\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas\strictplus\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas\automated1\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas\nogaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas\noallgaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas\gappyout\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas\strict\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas\strictplus\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas\automated1\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas\nogaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas\noallgaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas\gappyout\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas\strict\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas\strictplus\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas\automated1\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas\nogaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas\noallgaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas\gappyout\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas\strict\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas\strictplus\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas\automated1\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas\nogaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas\noallgaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas\gappyout\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas\strict\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas\strictplus\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas\automated1\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas\nogaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas\noallgaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas\gappyout\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas\strict\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas\strictplus\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas\automated1\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas\nogaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas\noallgaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas\gappyout\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas\strict\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas\strictplus\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas\automated1\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas\nogaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas\noallgaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas\gappyout\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas\strict\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas\strictplus\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas\automated1\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas\nogaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas\noallgaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas\gappyout\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas\strict\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas\strictplus\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas\automated1\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas\nogaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas\noallgaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas\gappyout\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas\strict\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas\strictplus\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas\automated1\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas\nogaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas\noallgaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas\gappyout\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas\strict\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas\strictplus\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas\automated1\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas\nogaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas\noallgaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas\gappyout\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas\strict\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas\strictplus\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas\automated1\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas\nogaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas\noallgaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas\gappyout\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas\strict\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas\strictplus\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas\automated1\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas\nogaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas\noallgaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas\gappyout\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas\strict\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas\strictplus\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas\automated1\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas\nogaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas\noallgaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas\gappyout\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas\strict\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas\strictplus\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas\automated1\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas\nogaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas\noallgaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas\gappyout\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas\strict\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas\strictplus\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas\automated1\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas\nogaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas\noallgaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas\gappyout\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas\strict\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas\strictplus\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas\automated1\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas\nogaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas\noallgaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas\gappyout\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas\strict\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas\strictplus\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas\automated1\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas\nogaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas\noallgaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas\gappyout\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas\strict\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas\strictplus\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas\automated1\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas\nogaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas\noallgaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas\gappyout\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas\strict\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas\strictplus\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas\automated1\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas\nogaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas\noallgaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas\gappyout\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas\strict\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas\strictplus\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas\automated1\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas\nogaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas\noallgaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas\gappyout\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas\strict\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas\strictplus\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas\automated1\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas\nogaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas\noallgaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas\gappyout\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas\strict\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas\strictplus\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas\automated1\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas\nogaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas\noallgaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas\gappyout\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas\strict\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas\strictplus\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas\automated1\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas\nogaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas\noallgaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas\gappyout\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas\strict\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas\strictplus\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas\automated1\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas\nogaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas\noallgaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas\gappyout\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas\strict\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas\strictplus\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas\automated1\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas\nogaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas\noallgaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas\gappyout\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas\strict\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas\strictplus\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas\automated1\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas\nogaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas\noallgaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas\gappyout\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas\strict\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas\strictplus\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas\automated1\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas\nogaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas\noallgaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas\gappyout\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas\strict\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas\strictplus\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas\automated1\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas\nogaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas\noallgaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas\gappyout\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas\strict\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas\strictplus\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas\automated1\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas\nogaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas\noallgaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas\gappyout\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas\strict\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas\strictplus\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas\automated1\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas\nogaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas\noallgaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas\gappyout\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas\strict\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas\strictplus\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas\automated1\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas\nogaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas\noallgaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas\gappyout\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas\strict\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas\strictplus\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas\automated1\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas\nogaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas\noallgaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas\gappyout\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas\strict\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas\strictplus\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas\automated1\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas\nogaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas\noallgaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas\gappyout\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas\strict\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas\strictplus\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas\automated1\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas\nogaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas\noallgaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas\gappyout\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas\strict\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas\strictplus\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas\automated1\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas\nogaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas\noallgaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas\gappyout\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas\strict\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas\strictplus\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas\automated1\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas\nogaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas\noallgaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas\gappyout\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas\strict\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas\strictplus\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas\automated1\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas\nogaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas\noallgaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas\gappyout\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas\strict\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas\strictplus\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas\automated1\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas\nogaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas\noallgaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas\gappyout\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas\strict\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas\strictplus\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas\automated1\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas\nogaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas\noallgaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas\gappyout\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas\strict\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas\strictplus\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas\automated1\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas\nogaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas\noallgaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas\gappyout\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas\strict\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas\strictplus\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas\automated1\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas\nogaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas\noallgaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas\gappyout\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas\strict\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas\strictplus\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas\automated1\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas\nogaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas\noallgaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas\gappyout\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas\strict\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas\strictplus\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas\automated1\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas\nogaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas\noallgaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas\gappyout\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas\strict\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas\strictplus\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas\automated1\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas\nogaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas\noallgaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas\gappyout\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas\strict\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas\strictplus\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas\automated1\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas\nogaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas\noallgaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas\gappyout\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas\strict\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas\strictplus\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas\automated1\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas\nogaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas\noallgaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas\gappyout\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas\strict\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas\strictplus\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas\automated1\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas\nogaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas\noallgaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas\gappyout\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas\strict\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas\strictplus\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas\automated1\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas\nogaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas\noallgaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas\gappyout\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas\strict\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas\strictplus\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas\automated1\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas\nogaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas\noallgaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas\gappyout\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas\strict\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas\strictplus\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas\automated1\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas\nogaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas\noallgaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas\gappyout\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas\strict\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas\strictplus\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas\automated1\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas\nogaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas\noallgaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas\gappyout\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas\strict\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas\strictplus\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas\automated1\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas\nogaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas\noallgaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas\gappyout\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas\strict\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas\strictplus\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas\automated1\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas\nogaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas\noallgaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas\gappyout\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas\strict\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas\strictplus\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas\automated1\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas\nogaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas\noallgaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas\gappyout\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas\strict\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas\strictplus\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas\automated1\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas\nogaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas\noallgaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas\gappyout\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas\strict\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas\strictplus\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas\automated1\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas\nogaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas\noallgaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas\gappyout\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas\strict\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas\strictplus\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas\automated1\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas\nogaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas\noallgaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas\gappyout\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas\strict\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas\strictplus\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas\automated1\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas\nogaps\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas\noallgaps\example.091.AA.strNOG.ENOG411BWBU.fasta