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Computational Biology & Evolution

Archive for the ‘tools’ tag

MetaPhOrs video tutorial (meta orthology prediction)

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Read more at the openHelix blog.

MetaPhOrs (Pryszcz, et al. 2010) is a public repository of phylogeny-based orthology and paralogy predictions that were computed using resources available in seven popular homology prediction services (PhylomeDB, EnsemblCompara, EggNOG, OrthoMCL, COG, Fungal Orthogroups, and TreeFam).

Written by jaime

June 1st, 2011 at 1:15 pm

Posted in Bioinformatics

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COURSE: Analysis and manipulation of phylogenomic data using the ETE python toolkit and TreeKo

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Organized by the Bioinformatics Core Facility at CRG and Toni Gabaldon’s lab.
Location: Centre for Genomic Regulation, Barcelona (Spain).
Duration: 3 days
Dates: April 6th- 8th (2011)
deadline: 15th of March
free registration (limitted places)

More info at http://ete.cgenomics.org/course_2011

Written by jaime

January 26th, 2011 at 3:29 pm

Posted in Bioinformatics

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PhylomeDB video tutorial

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Written by jaime

December 18th, 2010 at 3:59 pm

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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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