PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.

ABSTRACT:

Background

To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.

Results

Here, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i) the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii) the search for use

SUBMITTER: Gouret P 

PROVIDER: S-EPMC2759962 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature