Phylogeny.fr: robust phylogenetic analysis for the non-specialist.

Nucleic Acids Research
A DereeperO Gascuel

Abstract

Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users...Continue Reading

References

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Citations

Nov 28, 2012·Archives of Microbiology·Michel R Z PassariniLara D Sette
Mar 25, 2009·Journal of Molecular Evolution·D Adam MasonDavid S Goldfarb
Aug 3, 2010·Journal of Molecular Evolution·Marta MartinsPhilippe Silar
Jun 10, 2010·Applied Microbiology and Biotechnology·Caroline MirandeEvelyne Forano
Aug 21, 2012·Applied Microbiology and Biotechnology·Florence MartinYves Jouanneau
Oct 1, 2013·Applied Microbiology and Biotechnology·Loredano PollegioniGianluca Molla
Mar 20, 2013·Plant Cell Reports·Branka Salopek-SondiJutta Ludwig-Müller
Nov 18, 2010·Development Genes and Evolution·Kay HolstienApril Hill
Apr 25, 2012·Development Genes and Evolution·Paula Rezende-TeixeiraGláucia Maria Machado-Santelli
Aug 3, 2011·Parasitology Research·Sandra Karina MediciMartín Javier Eguaras
Aug 29, 2012·Parasitology Research·Myoung-Ro LeeWon-Ja Lee
Oct 27, 2010·Archives of Virology·Russell P GoodmanMax L Nibert
Jul 8, 2011·Archives of Virology·Ioannis E TzanetakisJing Zhou
Nov 15, 2011·Archives of Virology·Angelika ZieglerJörg Schubert
Aug 24, 2012·Archives of Virology·Mustafa M AbabnehMohammad B Al-Zghoul
Aug 23, 2012·Journal of Industrial Microbiology & Biotechnology·Alfonso MazuelosEduardo Villalobo
Mar 23, 2011·Biotechnology Letters·Jia Zeng, Jixun Zhan
Apr 24, 2009·Molecular and Cellular Biochemistry·Mathieu BoissanMarie-Lise Lacombe
May 20, 2011·Plant Molecular Biology·Rachel A Okrent, Mary C Wildermuth
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Feb 23, 2013·Plant Molecular Biology·Mrinalini MuralidharanTsafrir S Mor
Jan 1, 2012·Plant Molecular Biology Reporter·Joanna SzewińskaWiesław Bielawski

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Software Mentioned

Blastall
Protdist
Drawgram
ATV
MODELTEST
. fr
Neighbor
Consense
fr
Perl

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