SQUID

SQUID is Sean Eddy's C toolkit for some basic sequence and alignment IO. It provides several already written tools. This is included in HMMER so no need to install it separately unless you want the most up to date version of the library.

afetch

Retrieve an alignment from a database of alignments

alistat

Alignment statistics for a single or set of alignments.

compalign

Compare two sequence alignments - for RNA structure comparison.

compstruct

Compare two sequence secondary structures - for RNA structure comparison.

revcomp

Reverse complement sequences

seqsplit

Split a sequence into fragments

seqstat

Some simple sequence statistics for a single or database of sequences including average, min, and max length, and GC content (where appropriate).

sfetch

For use with sindex - fast random access to fetch a sequence from an indexed database of sequences.

sindex

Index a flatfile database of sequences for fast random access.

shuffle

Randomly shuffle the columns of an alignment or a sequence for use in assessing significance of an alignment or structure

sreformat

An all purpose sequence and alignment reformatted. The script bp_sreformat provides much of the same functionality - in particular the BioPerl system supports the NEXUS multiple alignment format which is not supported by SQUID.

translate

Translate a DNA sequence into protein, either in a particular frame or try and find ORFs

weight

Build a weight matrix from an alignment