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Computational Biology & Evolution

ETE 2.1 (beta) released. Visualize phylogenetic trees

A new version of ETE is available for testing. It includes many new features (specially in the tree visualization engine):

  • The programmable tree drawing engine has been rewritten to support circular tree visualization, better control on node graphical attributes, SVG, PDF and PNG rendering, and a module to create interative web tree images.
  • Support for new phylogenetic formats such as Phyloxml and Nexml support.
  • PhylomeDB v3 API is now included
  • Improved documentation system, including web tutorial and programming reference.
  • And a number of improvements and bug fixes

Check the releasing notes to download and start using the new version.

Written by jaime

July 1st, 2011 at 12:44 pm

Posted in Bioinformatics

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MetaPhOrs video tutorial (meta orthology prediction)

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

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

Written by jaime

December 18th, 2010 at 3:59 pm

Posted in Bioinformatics

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PhylomeDB 3

A new release of phylomeDB is out. It includes a number of changes, most notably the use of ETE v2.0 for online tree visualization and manipulation of trees and the use of unique ids for all hosted phylomes.

Try it at http://phylomedb.org

Written by jaime

September 15th, 2010 at 7:31 pm

Course: Analysis and manipulation of phylogenomic data using ETE

A three days practical course on ETE, entitled “Analysis and manipulation of phylogenomic data using ETE”, will be held in Portugal from June 23rd to June 25th. The course is organized by the Gabaldon’s lab at CRG and The Gulbenkian Training Programme in Bioinformatics (GTPB).

More info at:
http://ete.cgenomics.org/GTPB_course_2010
http://gtpb.igc.gulbenkian.pt/bicourses/

Written by jaime

April 24th, 2010 at 1:03 pm

Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation

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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The pea aphid genome and phylome

With the sequencing of the Acyrthosiphon pisum genome [1], aphid research enters the genome era. The reconstruction of the complete collection of evolutionary histories of aphid  genes and their homologues in other sequenced arthropods [2] has not only helped in the annotation of the genome sequence but has also already provided important insights into the evolution of this specialized hemipteran. In particular, we undertook a phylogenetic analysis for every protein of this species in a context 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. To our knowledge, this is the first time that such a reliable methodology has been applied in the annotation pipeline of a newly sequenced genome.

  1. Genome sequence of the pea aphid Acyrthosiphon pisum. International Aphid Genomics Consortium. PLoS Biol. 2010 Feb 23;8(2):e1000313.
  2. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. J. Huerta-Cepas, M. Marcet-Houben, M. Pignatelli, A. Moya and T. Gabaldón

Written by jaime

March 17th, 2010 at 11:20 am

Uniprot cross-references to PhylomeDB


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)

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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