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.
Retrieve an alignment from a database of alignments
Alignment statistics for a single or set of alignments.
Compare two sequence alignments - for RNA structure comparison.
Compare two sequence secondary structures - for RNA structure comparison.
Reverse complement sequences
Split a sequence into fragments
Some simple sequence statistics for a single or database of sequences including average, min, and max length, and GC content (where appropriate).
Index a flatfile database of sequences for fast random access.
Randomly shuffle the columns of an alignment or a sequence for use in assessing significance of an alignment or structure
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 a DNA sequence into protein, either in a particular frame or try and find ORFs
Build a weight matrix from an alignment