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

@article{citeulike:5811274, 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 user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other.CONCLUSION:PhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.}, author = {Gouret, Philippe and Thompson, Julie and Pontarotti, Pierre}, citeulike-article-id = {5811274}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-10-298}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19765311}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19765311}, day = {19}, doi = {10.1186/1471-2105-10-298}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {evolutionary\_biology, phylogenetics, phyloinformatics, tree\_comparison}, month = {September}, number = {1}, pages = {298+}, posted-at = {2009-09-24 06:06:56}, priority = {2}, title = {PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees}, url = {http://dx.doi.org/10.1186/1471-2105-10-298}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:5811274 L3 - citeulike-article-id:5811274 N2 - 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 user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other.CONCLUSION:PhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern. IS - 1 JF - BMC Bioinformatics SN - 1471-2105 TI - PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees VL - 10 SP - 298 KW - evolutionary_biology KW - phylogenetics KW - phyloinformatics KW - tree_comparison AU - Gouret, Philippe AU - Thompson, Julie AU - Pontarotti, Pierre PY - 2009/09/19/ UR - http://dx.doi.org/10.1186/1471-2105-10-298 ER -