Phylogeny.fr: robust phylogenetic analysis for the non-specialist
Alexis Dereeper,Valentin Guignon,Guillaume Blanc,Stéphane Audic,S. Buffet,François Chevenet,Jean-François Dufayard,Stéphane Guindon,Vincent Lefort,Magali Lescot,Jean-Michel Claverie,Olivier Gascuel +11 more
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TLDR
The Phylogeny.fr platform transparently chains programs to automatically perform phylogenetic analyses and 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.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 can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/read more
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SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
TL;DR: SeaView version 4 combines all the functions of the widely used programs SeaView and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.
Journal ArticleDOI
The tissue inhibitors of metalloproteinases (TIMPs): An ancient family with structural and functional diversity
Keith Brew,Hideaki Nagase +1 more
TL;DR: Tissue inhibitors of metalloproteinases (TIMPs) are widely distributed in the animal kingdom and the human genome contains four paralogous genes encoding TIMPs 1 to 4, and their range of activities has now been found to be broader as it includes the inhibition of several of the disintegrin-metallop proteinases, ADAMs and ADAMTSs.
Journal ArticleDOI
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses
Richard J. O'Connell,Michael R. Thon,Stéphane Hacquard,Stefan G. Amyotte,Jochen Kleemann,Maria F. Torres,Ulrike Damm,Ester Alvarenga Santos Buiate,Lynn Epstein,Noam Alkan,Janine Altmüller,Lucia Alvarado-Balderrama,Christopher Bauser,Christian Becker,Bruce W. Birren,Zehua Chen,Jaeyoung Choi,Jo Anne Crouch,Jonathan P. Duvick,Jonathan P. Duvick,Mark A. Farman,Pamela Gan,David I. Heiman,Bernard Henrissat,Richard J. Howard,Mehdi Kabbage,Christian Koch,Barbara Kracher,Yasuyuki Kubo,Audrey D. Law,Marc-Henri Lebrun,Yong-Hwan Lee,Itay Miyara,Neil Moore,Ulla Neumann,Karl Nordström,Daniel G. Panaccione,Ralph Panstruga,Ralph Panstruga,Michael Place,Robert H. Proctor,Dov Prusky,Gabriel E. Rech,Richard Reinhardt,Jeffrey A. Rollins,Steve Rounsley,Christopher L. Schardl,David C. Schwartz,Narmada Shenoy,Ken Shirasu,Usha Rani Sikhakolli,Kurt Stüber,Serenella A. Sukno,James A. Sweigard,Yoshitaka Takano,Hiroyuki Takahara,Hiroyuki Takahara,Frances Trail,H. Charlotte van der Does,H. Charlotte van der Does,Lars M. Voll,Isa Will,Sarah Young,Qiandong Zeng,Jingze Zhang,Shiguo Zhou,Martin B. Dickman,Paul Schulze-Lefert,Emiel Ver Loren van Themaat,Li-Jun Ma,Li-Jun Ma,Lisa J. Vaillancourt +71 more
TL;DR: Findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
Journal ArticleDOI
BLAST-EXPLORER helps you building datasets for phylogenetic analysis
TL;DR: BLAST-Explorer is an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of theBLAST results and flexible selection of homologous sequences among the BLAST hits.
Journal ArticleDOI
The microbiome of uncontacted Amerindians
Jose C. Clemente,Erica C. Pehrsson,Martin J. Blaser,Martin J. Blaser,Kuldip Sandhu,Zhan Gao,Bin Wang,Magda Magris,Glida Hidalgo,Monica Contreras,Oscar Noya-Alarcon,Orlana Lander,Jeremy McDonald,Michael J. Cox,Jens Walter,Phaik Lyn Oh,Jean F. Ruiz,Selena Rodriguez,Nan Shen,Se Jin Song,Jessica L. Metcalf,Rob Knight,Rob Knight,Gautam Dantas,M. Gloria Dominguez-Bello,M. Gloria Dominguez-Bello,M. Gloria Dominguez-Bello +26 more
TL;DR: It is suggested that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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