Dart Perl Scripts

Perl scripts in the DART library

Located in: dart/perl/

TODO: include Perl modules as well?

drop-gappy-columns.pl

Author: Andrew Uzilov

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).

foldplot.pl

NB: Requires GD (the CPAN module as well as libgd).

phylohmmgenerator.pl (in progress)

Authors: Ian Holmes, Gabriel Wu

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

seqdotplot.pl

NB: Requires GD (the CPAN module as well as libgd).

windowlicker.pl

See: Window Licker

xgram2hsm.pl

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-- Created by: Andrew Uzilov on 22 Aug 2006