esl-alipid - Man Page

calculate pairwise percent identities for all sequence pairs in an MSA


esl-alipid [options] msafile


esl-alistat calculates the pairwise percent identity of each sequence pair in in the MSA(s) in msafile. For each sequence pair, it outputs a line of <sqname1> <sqname2> <pid> <nid> <n> where <pid> is the percent identity, <nid> is the number of identical aligned pairs, and <n> is the denominator used for the calculation: the shorter of the two (unaligned) sequence lengths.

If msafile is - (a single dash), alignment input is read from  stdin.

Only canonical residues are counted toward <nid> and <n>. Degenerate residue codes are not counted.



Print brief help;  includes version number and summary of all options, including expert options.

--informat <s>

Assert that input msafile is in alignment format <s>, bypassing format autodetection. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. For more information, and for codes for some less common formats, see main documentation. The string <s> is case-insensitive (a2m or A2M both work).


Assert that the msafile contains protein sequences.


Assert that the msafile contains DNA sequences.


Assert that the msafile contains RNA sequences.

See Also



Nov 2020 Easel 0.48 Easel Manual