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Open Access Software

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

Davin Butt1, Andrew J Roger23 and Christian Blouin123*

Author Affiliations

1 Faculty of Computer Science, Dalhousie University, 6050 University Ave. Halifax, NS, B3H 1W5, Canada

2 Dept. of Biochemistry and Molecular Biology, Dalhousie University, Tupper Medical Building, Halifax, NS, B3H 1X5, Canada

3 Canadian Institute for Advanced Research (CIAR)

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BMC Bioinformatics 2005, 6:138  doi:10.1186/1471-2105-6-138

Published: 6 June 2005

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.