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Computational Biology & Evolution

Archive for the ‘Bioinformatics’ tag

ETE 2.1 (beta) released. Visualize phylogenetic trees

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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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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

Posted in Bioinformatics

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PhylomeDB 3

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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

The pea aphid genome and phylome

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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