I have updated my codon usage program GCUA. It is free for you to use and
available for download at:
GCUA performs many of the usual codon usage analyses, such as counting
codons, analysing base composition etc. It also has a number of
multivariate analysis functions and these can be used to analyse the codon
and amino acid composition of genomes. The current version is formatted for
a maximum of 50,000 genes, enough to analyse the human genome coding
regions. These genes can be up to a half a million bases in length. You
can also produce a PAUP or PHYLIP - compatible 'distance matrix' based on
codon composition (not on pairwise similarities of the sequences).
This is an excerpt from the history file.
Included function to calculate Effective Number of Codons (Wright, 1991).
Included the option of performing multivariate analyses on raw codon counts.
Allowed recognition of GDE formatted files.
Sequence names extended to 250 characters in length.
Modified the ADE output settings.
Corrected bug in calculating base composition.
Increased the amount of sequence data that can be analysed (50,000 sequences
x 500,000 bp).
Modified the memory requirements.
Dr. James O. McInerney,
Bioinformatics and Pharmacogenomics Laboratory,
Department of Biology, National University of Ireland,
Maynooth, Co. Kildare, Ireland.
P:+353 1 708 3860
F:+353 1 708 3845
M:+353 87 6480102
E:james.o.mcinerney at may.iehttp://www.may.ie/academic/biology/jmbioinformatics.shtmlhttp://www.bioinf.org/