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BMC Bioinformatics. 2005 Jun 6;6:138.

libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.

Author information

1
Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada. davin@cs.dal.ca

Abstract

BACKGROUND:

An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task.

RESULTS:

The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications.

CONCLUSION:

Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

PMID:
15938750
PMCID:
PMC1175080
DOI:
10.1186/1471-2105-6-138
[Indexed for MEDLINE]
Free PMC Article
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