1esl-alipid(1)                    Easel Manual                    esl-alipid(1)
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NAME

6       esl-alipid  -  calculate  pairwise  percent identities for all sequence
7       pairs in an MSA
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SYNOPSIS

11       esl-alipid [options] msafile
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DESCRIPTION

16       esl-alistat calculates the pairwise percent identity of  each  sequence
17       pair in in the MSA(s) in msafile.  For each sequence pair, it outputs a
18       line of <sqname1> <sqname2> <pid> <nid> <n> where <pid> is the  percent
19       identity,  <nid>  is  the number of identical aligned pairs, and <n> is
20       the denominator used for the calculation: the shorter of the  two  (un‐
21       aligned) sequence lengths.
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24       If msafile is - (a single dash), alignment input is read from stdin.
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27       Only  canonical  residues are counted toward <nid> and <n>.  Degenerate
28       residue codes are not counted.
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OPTIONS

32       -h     Print brief help;  includes version number and  summary  of  all
33              options, including expert options.
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36       --informat <s>
37              Assert  that input msafile is in alignment format <s>, bypassing
38              format autodetection.  Common choices for  <s>  include:  stock‐
39              holm,  a2m,  afa,  psiblast, clustal, phylip.  For more informa‐
40              tion, and for codes for some less common formats, see main docu‐
41              mentation.   The string <s> is case-insensitive (a2m or A2M both
42              work).
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45       --amino
46              Assert that the msafile contains protein sequences.
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49       --dna  Assert that the msafile contains DNA sequences.
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52       --rna  Assert that the msafile contains RNA sequences.
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SEE ALSO

58       http://bioeasel.org/
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62       Copyright (C) 2020 Howard Hughes Medical Institute.
63       Freely distributed under the BSD open source license.
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AUTHOR

67       http://eddylab.org
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71Easel 0.48                         Nov 2020                      esl-alipid(1)
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