esl-weight - Man Page

esl-weight [options] msafile

esl-weight calculates individual sequence weights for each alignment in msafile and outputs a new  multiple sequence alignment file in Stockholm format with the weights annotated in Stockholm-format  #=GS seqname WT weight lines. The default weighting algorithm is the Gerstein/Sonnhammer/Chothia algorithm.

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

-h

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

-g

Use the Gerstein/Sonnhammer/Chothia weighting algorithm; this is the default.

-p

Use the Henikoff position-based weighting algorithm. This is faster and more memory efficient than the default.

-b

"BLOSUM weights": use approximately the same rule used in constructing the BLOSUM score matrices. This involves single-linkage clustering at some fractional identity threshold (default 0.62; see --id option), then for each cluster, splitting a total weight of one uniformly amongst all sequences in the cluster.

--id <x>

Sets the fractional identity threshold used by the BLOSUM weighting rule (option -b; required), to a number 0<=x<=1. Default is 0.62.

--amino

Assert that the msafile contains protein sequences.

--dna

Assert that the msafile contains DNA sequences.

--rna

Assert that the msafile contains RNA sequences.

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Copyright (C) 2020 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.

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