Esta semana inició el curso de métodos filogenéticos de la WHS en Xalapa

Este Lunes 23 de Mayo inicio el taller de la WHS en el INECOL, Xalapa.
El curso despertó mucho interés y asisten 25 participantes de varios países: EUA, Mexico, Costa Rica, Colombia, Perú, Brasil, Argentina y España!
Varias fotos del grupo están en la Galería en el sito web del curso aquí.

En la foto arriba, John Wenzel a cargo de las clases el Lunes. Entre él y Kevin Nixon (foto abajo) impartieron las clases y prácticas del Lunes y Martes.



La tarde del Martes fuimos a un restaurant local para cenar como grupo. Disfrutamos de buena comida mexicana y un ambiente muy agradable con viejos y nuevos amigos. Para algunos la noche terminó en un karaoke muy revelador de habilidades vocales y musicales!



El taller sigue esta semana hasta el viernes. Miércoles y Jueves Ward Wheeler y Viernes con Chris Randle.

Junio 6, PD: Me informan que el viernes por la noche también hubo karaoke! Sin duda, todo un exito el taller!

La Galeria del curso esta en:
http://www.filogenetica.org/cursos/WHSphotos/Gallery/

Computational phyloinformatics workshop. Kyoto

Computational Phyloinformatics is an 11-day intensive summer workshop co-sponsored by the Bioinformatics Center of Kyoto University, DBCLS/JST and NESCent, and will take place at the Bioinformatics Center in Kyoto, Japan following the SMBE 2011 meeting.

The workshop aims to give biologists practical knowledge and hands-on programming skills in phyloinformatics.

Instructors and Course Organizers

• Christian Zmasek (Sanford-Burnham Medical Research Institute; Functional Genomics with BioRuby)
• Karen Cranston (NESCent Training Coordinator)
• Rutger A. Vos (University of Reading; Phyloinformatics with BioPerl and Bio::Phylo)
• Susumu Goto (Bioinformatics Center, KEGG laboratory)
• Toshiaki Katayama (Human Genome Center, University of Tokyo)
• William H. Piel (Yale Peabody Museum; Phyloinformatics with SQL)

MORE INFORMATION >>>

Faster exact maximum parsimony search with XMP

W. Timothy J. White1, and Barbara R. Holland. 2011. Faster exact maximum parsimony search with XMP. Bioinformatics (2011) 27 (10): 1359-1367. doi: 10.1093/bioinformatics/btr147 First published online: March 27, 2011


Abstract

Motivation: Despite trends towards maximum likelihood and Bayesian criteria, maximum parsimony (MP) remains an important criterion for evaluating phylogenetic trees. Because exact MP search is NP-complete, the computational effort needed to find provably optimal trees skyrockets with increasing numbers of taxa, limiting analyses to around 25–30 taxa. This is, in part, because currently available programs fail to take advantage of parallelism.

Results: We present XMP, a new program for finding exact MP trees that comes in both serial and parallel versions. The serial version is faster in nearly all tests than existing software. The parallel version uses a work-stealing algorithm to scale to hundreds of CPUs on a distributed-memory multiprocessor with high efficiency. An optimized SSE2 inner loop provides additional speedup for Pentium 4 and later CPUs.

Availability: C source code and several binary versions are freely available from http://www.massey.ac.nz/~wtwhite/xmp.
The parallel version requires an MPI implementation, such as the freely available MPICH2.

Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis

BIO::Phylo-phyloinformatic analysis using perl
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen, Chase Miller.
BMC Bioinformatics 2011, 12:63
http://www.biomedcentral.com/1471-2105/12/63
open access

Abstract

Background

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.

Results

This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided.

Conclusions

Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo