esl-weight - Man Page

calculate sequence weights in MSA(s)


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.



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


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


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


"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.

Expert Options

--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.


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