README.rdoc in egor-0.0.4 vs README.rdoc in egor-0.0.5
- old
+ new
@@ -32,11 +32,11 @@
== OPTIONS:
--tem-file (-f) FILE: a tem file
--tem-list (-l) FILE: a list for tem files
--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
--outfile (-o) FILE: output filename (default 'allmat.dat')
- --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting
- --noweight: calculate substitution counts with no weights (default)
+ --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
+ --noweight: calculate substitution counts with no weights
--smooth (-s) INTEGER:
0 for parial smoothing (default)
1 for full smoothing
--nosmooth: perform no smoothing operation
--cys (-y) INTEGER: