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libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
Davin Butt1, Andrew J Roger, Christian Blouin
1Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada. davin@cs.dal.ca
BMC Bioinformatics
|June 9, 2005
Summary
The libcov bioinformatics library simplifies phylogenetic analysis using maximum likelihood. This C++ collection enables rapid development of new sequence analysis and protein phylogenetics methods.
Area of Science:
- Bioinformatics
- Computational Biology
- Phylogenetics
Background:
- Bioinformatics methods increasingly incorporate phylogenetic relationships.
- Maximum likelihood phylogenetic framework implementation is time-intensive.
Purpose of the Study:
- To introduce libcov, a C++ bioinformatics library.
- To facilitate rapid prototyping of phylogenetic analysis tools.
Main Methods:
- Development of a C++ class collection.
- Provision of high and low-level interfaces for phylogenetic analyses.
- Integration of sequence analysis and structural biology data structures.
Main Results:
- libcov offers functionalities for computing likelihoods, searching tree topologies, and estimating site rates.
- The library supports sequence clustering, tree manipulation, and phylogeny comparison.
- It provides a versatile data structure for structural biological methods.
Conclusions:
- libcov enables rapid development of applications leveraging phylogenetic likelihoods.
- It reduces the need for extensive software engineering efforts.
- The library is a valuable resource for developing in-house protein phylogenetics methodologies.