TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
TLDR
TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.Abstract:
Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experienceread more
Citations
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stéphane Guindon,Jean-François Dufayard,Vincent Lefort,Maria Anisimova,Wim Hordijk,Olivier Gascuel +5 more
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
Journal ArticleDOI
A Rapid Bootstrap Algorithm for the RAxML Web Servers
TL;DR: This work developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms and can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses.
Journal ArticleDOI
Tunicates and not cephalochordates are the closest living relatives of vertebrates
TL;DR: It is shown that phylogenetic analyses of the genome sequencing of the appendicularian Oikopleura dioica provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates.
Journal ArticleDOI
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
TL;DR: The phylogenetic terrace aware (PTA) data structure is introduced for the efficient analysis under partition models and it is shown that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ- TREE and RAxML implementations, respectively.
Journal ArticleDOI
The genome of Tetranychus urticae reveals herbivorous pest adaptations
Miodrag Grbic,Miodrag Grbic,Thomas Van Leeuwen,Richard M. Clark,Stephane Rombauts,Pierre Rouzé,Vojislava Grbic,Vojislava Grbic,Edward J. Osborne,Wannes Dermauw,Phuong Cao Thi Ngoc,Félix Ortego,Pedro Hernández-Crespo,Isabel Diaz,Manuel Martinez,Maria Navajas,Élio Sucena,Élio Sucena,Sara Magalhães,Lisa M. Nagy,Ryan M. Pace,Sergej Djuranovic,Guy Smagghe,Masatoshi Iga,Olivier Christiaens,Jan A. Veenstra,John Ewer,Rodrigo Mancilla Villalobos,Jeffrey L. Hutter,Stephen D. Hudson,Marisela Vélez,Marisela Vélez,Soojin V. Yi,Jia Zeng,Andre Pires-daSilva,Fernando Roch,Marc Cazaux,Marie Navarro,Vladimir Zhurov,Gustavo Acevedo,Anica Bjelica,Jeffrey A. Fawcett,Jeffrey A. Fawcett,Eric Bonnet,Eric Bonnet,Cindy Martens,Guy Baele,Lothar Wissler,Aminael Sánchez-Rodríguez,Luc Tirry,Catherine Blais,Kristof Demeestere,Stefan R. Henz,T. Ryan Gregory,Johannes Mathieu,Lou Verdon,Laurent Farinelli,Jeremy Schmutz,Erika Lindquist,René Feyereisen,Yves Van de Peer +60 more
TL;DR: The Tetranychus urticae genome is the smallest known arthropod genome as discussed by the authors, which represents the first complete chelicerate genome for a pest and has been annotated with genes associated with feeding on different hosts.
References
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Journal ArticleDOI
Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
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