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

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.

Figure 1

The likelihood of a consensus tree. In this example, a file containing trees in NEWICK format is parsed and a consensus tree is resolved using the greedy majority-rule consensus algorithm [9, 21]. Finally, the likelihood of the resulting tree is calculated. Bolded lines are libcov API calls.