Utilities

All tools listed below require the Perl Package
 
Alicut
 
Uses the Aliscore output and removes ambiguously aligned positions from sequence alignments. Paired positions can be considered if a dot-bracket structure is provided as the first string in the alignment.
 
Countbrackets
 
Converts a dot-bracket structure string into a list of paired and unpaired positions. This is useful to provide secondary structure information for MrBayes. Input is a plain textfile, which must only contain the dot-bracket structure string.
Usage: countbrackets.pl FILE