src

Software used for birdscanner

• Last modified: ons apr 22, 2020 12:19
• Sign: JN

Public software

• grepfasta.pl (provided, https://github.com/nylander/grepfasta)
• hmmerbuild, hmmpress, nhmmer (hmmer v.3.2.1, http://hmmer.org/)
• makeblastdb (ncbi-blast+ v.2.6.0+, https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs)
• parallel (https://www.gnu.org/software/parallel/)
• pigz (https://zlib.net/pigz/)
• plast (plast v.2.3.1, https://plast.inria.fr/plast-algorithm/)
• splitfast_100K (provided, https://github.com/nylander/Split_fasta_file)

In-house software

• create_nhmmer_slurm_file.pl
• degap_fasta.pl
• fasta2stockholm.pl
• fasta_unwrap.pl
• fasta_wrap.pl
• parse_nhmmer.pl
• remove_gaps_in_fasta.pl

Optional software

• astral (https://github.com/smirarab/ASTRAL)
• get_fasta_info.pl (https://github.com/nylander/get_fasta_info)
• iqtree (http://www.iqtree.org/)
• mafft (https://mafft.cbrc.jp/alignment/software/)
• odseq (https://github.com/PeterJehl/OD-Seq)
• oi.sh (provided)
• gather_genes.pl (provided)
• remove_gapped_seqs_in_fasta.pl (provided)