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ScripTree: scripting phylogenetic graphics

François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen, Vincent Berry
2010 Computer applications in the biosciences : CABIOS  
Scripting phylogenetic graphics would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks.  ...  Phylogenetic graphics instructions, related to tree rendering as well as tree annotation, are stored in a text file and processed in a sequential way.  ...  CONCLUSION ScripTree is a tool for scripting phylogenetic graphics. It allows the management of multiple trees and usual kinds of annotations.  ... 
doi:10.1093/bioinformatics/btq086 pmid:20194627 fatcat:c2y57awskfdzpkii5wztmwsa3m

A New Web Server for the Rapid Identifi cation of Microorganisms

Olivier Croce, François Chevenet, Richard Christen
2010 Journal of Microbial & Biochemical Technology  
The server also includes online software to automatically display annotated phylogenetic trees.  ...  It allows retrieving related sequences and their taxonomies, in order to proceed to phylogenetic analyses.  ...  Annotations are provided from a local database and through a pipeline that uses ScripTree (Chevenet et al., 2010) . ScripTree is a tool for scripting phylogenetic graphics.  ... 
doi:10.4172/1948-5948.1000029 fatcat:4p2ne7hbajgtbcc53lvzjqytga

CompPhy: a web-based collaborative platform for comparing phylogenies

Nicolas Fiorini, Vincent Lefort, François Chevenet, Vincent Berry, Anne-Muriel Arigon Chifolleau
2014 BMC Evolutionary Biology  
Conclusions: CompPhy is the first web platform devoted to the comparison of phylogenetic trees allowing real-time distant collaboration on a phylogenetic/phylogenomic project.  ...  The ScripTree interpreter for phylogenetic graphics is in charge of generating tree pictures [7] . It manages tree edition and annotation.  ...  ScripTree takes text files as input to produce a tree picture: the tree in Newick format, a script for the graphical rendering and annotations in CSV format.  ... 
doi:10.1186/s12862-014-0253-5 pmid:25496383 pmcid:PMC4271409 fatcat:ddq7tzg4tvfyzgknvgqfeqirje

Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations

Etienne Lord, Mickael Leclercq, Alix Boc, Abdoulaye Baniré Diallo, Vladimir Makarenkov, Simon Joly
2012 PLoS ONE  
A number of important phylogenetic and general bioinformatics tools have been included in the first software release.  ...  In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations.  ...  On the other hand, a graphical Table 2 .  ... 
doi:10.1371/journal.pone.0029903 pmid:22253821 pmcid:PMC3256230 fatcat:3bn34nd4prbn7fca3vbsty63qe

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

Sophie S. Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
2018 Frontiers in Microbiology  
Phylogenetic 32 analyses based on ribosomal proteins place the organism as a sister group to all known 33 mesophilic AOA. The 1.58 Mb genome of Ca.  ...  ScripTree: scripting 813 phylogenetic graphics.  ...  The pivotal phylogenetic position of Ca.  ... 
doi:10.3389/fmicb.2018.00028 pmid:29434576 pmcid:PMC5797428 fatcat:frbtb3wpufbq3h7oaytbaya4yq

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome [article]

Sophie S Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
2017 bioRxiv   pre-print
Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca.  ...  ScripTree: scripting 813 phylogenetic graphics.  ...  The pivotal phylogenetic position of Ca.  ... 
doi:10.1101/240879 fatcat:4ai6z7dcpnbcnii7v2nbyvbo2a

On building and comparing trees Application to supertrees in phylogenetics

Vincent Berry, Vincent, Académie De Montpellier
2009 unpublished
Christen concerning a scripting language for graphical display of phylogenetic trees that the former is currently developing.  ...  An application note on ScripTree should be submitted in the following month to the Bioinformatics journal.  ... 
fatcat:kzulocavzjac5htps7gbmmoyk4