MUSCLE is multiple alignment software for protein and nucleotide sequences.
The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.
Citation:
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.
The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.
The NCBI (National Center for Biotechnology Information) development toolkit,
containing various libraries needed by NCBI applications, as well as a
software suite containing, amongst other things, NCBI BLAST 2.0.
From the README:
The NCBI Software Development Toolkit was developed for the production and
distribution of GenBank, Entrez, BLAST, and related services by NCBI. We
make it freely available to the public without restriction to facilitate
the use of NCBI by the scientific community. However, please understand
that while we feel we have done a high quality job, this is not commercial
software.
The documentation lags considerably behind the software and we must make
any changes required by our data production needs. Nontheless, many people
have found it a useful and stable basis for a number of tools and
applications.
Bio::SCF module allows you to read and update (in a restricted
way) SCF chromatographic sequence files. It is an interface to
Roger Staden's io-lib. See the installation directions for further
instructions.
"The SEQIO package is a set of C functions which can read and write
biological sequence files formatted using various file formats and which
can be used to perform database searches on biological databases."
- from the README file
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It has an easy to use interface and currently features over 4000 different
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