Sequence View

The primary function of the Sequence View is to permit a visual inspection of the quality of the final alignment to ensure that there are no unexpected gaps, insertions, etc. in the alignment. An improper alignment will greatly impact determination of genetic distances and thus also the inferred network or phylogenetic tree. This may be especially true for non-HIV sequences, since the aligner in MicrobeTrace is not configured to handle sequences from pathogens other than HIV-1. Non-HIV-1 sequences may not always properly align using the TN93 nucleotide substitution model that is commonly used for HIV-1. The Sequence View may have limited value if a pre-aligned FASTA file is used in the analysis unless the Sequence View is used to re-check that alignment.

IMPORTANT NOTE: We strongly recommend checking the quality of all pre-made alignments prior to using them in MicrobeTrace. Also, please do not use MicrobeTrace to align a pre-aligned sequence, which may change the alignment. Please note that any edits made to the alignment in the sequence viewer will not automatically be rendered in the inferred network. The edited sequence alignment file must first be saved and can then be used from the beginning of the analysis in MicrobeTrace at the file loading step.

The image below shows the Sequence View displaying the aligned nucleotide sequences. Dialog boxes allow you to change the alignment appearance and to export the alignment.