Perl scripts in the DART library

Located in: dart/perl/

TODO: include Perl modules as well?

colorstock.pl

constock.pl

copy2stderr.pl

dartlog.pl

drop-gappy-columns.pl

Author: AndrewUzilov

Tool for dropping columns above a user-specified gap threshold from a Stockholm alignment. Also can:

• only replace the per-column annotation for the gappy columns with a user-specified symbol, but not drop them;
• drop columns containing user-specified annotation;
• run in RNA mode - for every gappy column dropped/changed, also drop/change the column to which it is base-paired (works on pseudoknotted secondary structures, as long as they are annotated by the Rfam convention).

fancyeisen.pl

fasta2stockholm.pl

foldplot.pl

hsm2xgram.pl

hsmplot.pl

iteridem.pl

ka_ks.pl

majorcons.pl

old_xrate.pl

pandit2stockholm.pl

percentid.pl

phylogramTool.pl

phylohmmgenerator.pl (in progress)

Authors: IanHolmes, GabrielWu

Generates an xgram grammar file for measuring relative rates of residue evolution in proteins.

sanebp.pl

seqdotplot.pl

splitstock.pl

sscolorMult.pl

sscolor.pl

stkCompareAnnot.pl

stockholm2ct.pl

stockholm2fasta.pl

testharness.pl

trapper.pl

trimstock.pl

windowlicker.pl

See: WindowLicker

xgram2hsm.pl

-- Created by: AndrewUzilov on 22 Aug 2006