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Computational Biology & Evolution

Archive for the ‘phylogeny’ tag

Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation

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This 5-days course involves theoretical and computer practicals sessions that address different problems of evolutionary biology and hypothesis testing. The course includes a session of phylogenomic analysis and functional annotation, including most recent developments in these areas. Attendees will get familiar with, among others, the following tools: Phylip, Phyml, PAML, TreePuzzle, MrBayes, Modeltest, ProTest, jModelTest programs, all of them integrated in the Phylemon web-server. The course is intended for professional biologists or chemists whose work involves the analyses of biological sequences.

The course will be held from 14th to 18th of June (2010), at Valencia, Spain.
More info at: http://bioinfo.cipf.es/courses/mol_evol_phylo_5ed/

Written by jaime

April 23rd, 2010 at 1:24 pm

Posted in Bioinformatics

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Uniprot cross-references to PhylomeDB

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UniProt release 15.11 (Published November 24, 2009)
Cross-references have been added to PhylomeDB, a database for complete collections of gene phylogenies. PhylomeDB allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.

Source: http://www.uniprot.org/news/2009/11/24/release

Written by jaime

December 11th, 2009 at 3:21 pm

Posted in Bioinformatics

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ETE v2 released (a python toolkit to deal with phylogenetic trees)

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ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees [1]. It provides a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. It supports large tree data structures, node annotation, independent editing and analysis of tree partitions and the association of trees with external data such as multiple sequence alignments or numerical matrices.

  1. ETE: a python Environment for Tree Exploration Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón.  BMC Bioinformatics 2010, 11:24doi:10.1186/1471-2105-11-24

If you work on phylogenetics and use python for writing your programs, check this program out at http://ete.cgenomics.org

Written by jaime

November 12th, 2009 at 12:50 pm

Posted in Bioinformatics

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