title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS, B3H 1W5, Canada. davin@cs.dal.ca
authors.forename: Davin
authors.initials: D
authors.lastname: Butt
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Roger
authors.forename: Christian
authors.initials: C
authors.lastname: Blouin
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D003201:Computers; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D019143:Evolution, Molecular; D015723:Gene Library; D016013:Likelihood Functions; D010802:Phylogeny; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D012985:Software Design