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Unité Mixte de Recherche Inra-Univ. Bordeaux 1 "Biodiversité Gènes et Communautés" - Biogeco

Unité mixte de recherche (Inra, Univ. Bordeaux 1)Biodiversité, gènes et communautés (Biogeco) INRA_rvb150Bordeaux1

INRA Bordeaux-Aquitaine

Site de Recherches Forêt-Bois

69 route d'Arcachon

33612 CESTAS Cedex - FRANCE

Phylorph

PHYLORPH - PHYLogenetic markers for ORPHan species

PHYLORPH aims to screen fungal genomic databases (107 full genome sequences available in ver. 2.0) for single copy genes that might be easily transferable and well suited for evolutionary studies in non-model fungal species. To maximize the chance to target genes with phylogenetically informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relatively to substitution type. PHYLORPH is Windows application written in Python (ver. 2.6) controlled with a graphical interface developed with the WxPython module.

Installation

Version 2.0 can be downloaded here and unzipped in a folder named PHYLORPH. Upon clicking on the PHYLORPH.exe icon, PHYLORPH executes itself the installation by downloading the BLAST and MUSCLE programs and creating all required directories into the PHYLORPH folder. Additional help is provided with the program file. See also Getting started.

Related publications

Feau, N., Dutech, C., Decourcelle, T., Fabreguettes, O., Desprez-Loustau, M-L. 2011. finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi. PLoS ONE 6(4): e18803. See also our poster presented at the IMC9 meeting

Author

Please, send questions/comments/suggestions to Nicolas Feau, nfeau_at_bordeaux.inra.fr

Updates

March, 4th 2011. Version 2.0. Two additional protein datasets orthologs added: PHYLOME-T60 and OrthoMCL-DB. The three ortholog repositories (FUNYBASE, PHYLOME-T60 and OrthoMCL-DB) represent a potential of 329 different markers which can be used to interrogate 107 fungal genome sequences.

November, 23th 2010. Version 1.0. Five new genomes added: Mycosphaerella populorum(anamorph: Septoria musiva;Capnodiales, Dothideomycetes), Pichia angusta (Saccharomycetales, Saccharomycetes), Rhodotorula graminis (Sporidiales, Uredinomycetes), Gleophyllumtrabeum (Gleophyllales, Agaricomycetes) and Wallemia sebi (Wallemiales, Wallemiomycetes).

November, 12th 2010. Version 1.0. Four new genomes added: Geomycesdestructans (Helotiales, Leotiomycetes), Talaromyces stipitatus (Eurotiales, Eurotiomycetes), Microbotryum violaceum (Microbotryales, Microbotryomycetes) and Mycosphaerella pini (anamorph: Dothistroma septosporum; Capnodiales, Dothideomycetes).

***Note that loading of the Talaromyces stipitatus, Grosmania clavigera and Blumeria graminis genomes (from NCBI) may be long.***