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

6       esl-weight - calculate sequence weights in MSA(s)
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SYNOPSIS

10       esl-weight [options] msafile
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DESCRIPTION

14       esl-weight calculates individual sequence weights for each alignment in
15       msafile and outputs a new multiple sequence alignment file in Stockholm
16       format  with  the weights annotated in Stockholm-format #=GS seqname WT
17       weight lines.  The default weighting algorithm is the Gerstein/Sonnham‐
18       mer/Chothia algorithm.
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21       If msafile is - (a single dash), MSA input is read from stdin.
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OPTIONS

28       -h     Print  brief  help;   includes version number and summary of all
29              options, including expert options.
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32       -g     Use the Gerstein/Sonnhammer/Chothia weighting algorithm; this is
33              the default.
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36       -p     Use  the  Henikoff  position-based  weighting algorithm. This is
37              faster and more memory efficient than the default.
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40       -b     "BLOSUM weights": use approximately the same rule used  in  con‐
41              structing  the BLOSUM score matrices. This involves single-link‐
42              age clustering at some fractional  identity  threshold  (default
43              0.62; see --id option), then for each cluster, splitting a total
44              weight of one uniformly amongst all sequences in the cluster.
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EXPERT OPTIONS

49       --id <x>
50              Sets the  fractional  identity  threshold  used  by  the  BLOSUM
51              weighting  rule  (option -b; required), to a number 0<=x<=1. De‐
52              fault is 0.62.
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55       --amino
56              Assert that the msafile contains protein sequences.
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59       --dna  Assert that the msafile contains DNA sequences.
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62       --rna  Assert that the msafile contains RNA sequences.
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SEE ALSO

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

75       http://eddylab.org
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79Easel 0.48                         Nov 2020                      esl-weight(1)
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