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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

S. Guindon, F. Lethiec, P. Duroux, O. Gascuel
2005 Nucleic Acids Research  
PHYML Online is a web interface to PHYML, a software that implements a fast and accurate heuristic for estimating maximum likelihood phylogenies from DNA and protein sequences.  ...  The server and its documentation are available from http://atgc.lirmm.fr/phyml.  ...  S.G. is supported by a postdoctoral fellowship from the Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand.  ... 
doi:10.1093/nar/gki352 pmid:15980534 pmcid:PMC1160113 fatcat:me4eq57gkfftteaw3a72saebuu

Applications and Algorithms for Inference of Huge Phylogenetic Trees: a Review

Muhammad Sardaraz, Muhammad Tahir, Tahir Aziz Ikram, Hassan Bajwa
2012 American Journal of Bioinformatics Research  
This article presents a comprehensive survey of the applications and the algorithms for inference of huge phylogenetic trees and also gives the reader an overview of the methods currently employed for  ...  the inference of phylogenetic trees.  ...  [38] present a program for mining online databases, sequence alignment and phylogenetic trees. The program is based on ML, Distance Method and Maximum Parsimony Method.  ... 
doi:10.5923/j.bioinformatics.20120201.04 fatcat:cwskdp7b6ze6xdlq5qekgypjwm

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

2019 Nucleic Acids Research  
maximum likelihood and Bayesian).  ...  These tools cover a large range of usage (sequence searching, multiple sequence alignment, model selection, tree inference and tree drawing) and a large panel of standard methods (distance, parsimony,  ...  ACKNOWLEDGEMENTS We thank the 'Genome Informatics and Phylogenetics' (GI-Phy) expertise group of Institut Pasteur for helpful discussions and testing, as well as the IT System Department of Institut Pasteur  ... 
doi:10.1093/nar/gkz303 pmid:31028399 pmcid:PMC6602494 fatcat:elwfebkvdffdxkw3hwokgluqdm

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites

Wenjie Deng, Brandon Maust, David Nickle*, Gerald Learn**, Yi Liu, Laura Heath, Sergei Kosakovsky Pond, James Mullins
2010 BioTechniques  
Mittler for discussions. This work was supported by grants from the US Public Health Services (grant nos.  ...  AI047734 and AI057005), including support to the Computational Biology Core of the University of Washington Center for AIDS Research (grant no. AI27757).  ...  For example, PhyML Online (1) performs maximum likelihood (ML) phylogenetic estimation under a wide range of evolutionary models.  ... 
doi:10.2144/000113370 pmid:20569214 pmcid:PMC3133969 fatcat:qp64ylqudvc7neybxpdk4bn7ee

A Rapid Bootstrap Algorithm for the RAxML Web Servers

Alexandros Stamatakis, Paul Hoover, Jacques Rougemont, Susanne Renner
2008 Systematic Biology  
ACKNOWLEDGMENTS We would like to thank Tandy Warnow, who initiated this work by requesting a quick and dirty BS algorithm, Peter Waddell for discussions about RELL, and Jakob Fredslund for providing us  ...  Finally, we would like to thank Olivier Gascuel and an anonymous reviewer for useful comments on the manuscript.  ...  Web servers.-There already exist several Web servers for inference of phylogenetic trees.  ... 
doi:10.1080/10635150802429642 pmid:18853362 fatcat:dhwonxrgtbdwbnnqkbtm3k6gyy

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey, Erik van Nimwegen
2014 Molecular biology and evolution  
, 2) extract single nucleotide polymorphisms (SNPs), and 3) infer the phylogenetic tree using maximum likelihood methods from the aligned SNP positions.  ...  We implemented this method as a web server named REALPHY (Reference sequence Alignment-based Phylogeny builder), which fully automates phylogenetic reconstruction from raw sequencing reads.  ...  Acknowledgment The authors thank Chris Field for helpful discussions.  ... 
doi:10.1093/molbev/msu088 pmid:24600054 pmcid:PMC3995342 fatcat:wgozyz3euves7c6nqqqxxletgu

primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies

B. Contreras-Moreira, B. Sachman-Ruiz, I. Figueroa-Palacios, P. Vinuesa
2009 Nucleic Acids Research  
values of maximum likelihood phylogenies.  ...  Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized  ...  Romualdo Zayas-Laguna and Vı´ctor del Moral are acknowledged for their technical help.  ... 
doi:10.1093/nar/gkp377 pmid:19465390 pmcid:PMC2703966 fatcat:rcz6e7m3tbeu5bjjqdq3py5efi

Detection and Analysis of Non-retroviral RNA Virus-Like Elements in Plant, Fungal, and Insect Genomes [chapter]

Hideki Kondo, Sotaro Chiba, Nobuhiro Suzuki
2014 Msphere  
Enodogenous non-retroviral RNA like sequences (NRVSs) have been discovered in the genome of a wide range of eukaryotes.  ...  Discovery of the novel NRVSs and understanding of their phylogenetic relationship with modern viral relatives provide important information on deep evolutionary history of RNA virus-host interactions.  ...  PhyML 3.0, a tool for estimating maximum-likelihood (ML) phylogenies (at http://www.atgc-montpellier.fr/phyml/) (18).  ... 
doi:10.1007/978-1-4939-1743-3_7 pmid:25287497 fatcat:6qmxzeg72jgofalwazlmmzovdy

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

Vagner Fonseca, Pieter J. K. Libin, Kristof Theys, Nuno R. Faria, Marcio R. T. Nunes, Maria I. Restovic, Murilo Freire, Marta Giovanetti, Lize Cuypers, Ann Nowé, Ana Abecasis, Koen Deforche (+12 others)
2019 PLoS Neglected Tropical Diseases  
Available online: http://krisp.org.za/tools.php.  ...  This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome  ...  The web application that makes our tool available through an easy-touse web interface is available online via a dedicated server that is hosted at http://www.krisp. org.za/tools.php.  ... 
doi:10.1371/journal.pntd.0007231 pmid:31067235 pmcid:PMC6527240 fatcat:njhzjpmbf5ep7h27oxrzw4cm4i

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.  ...  Acknowledgments The authors are thankful to the editor Simon Joly and to two anonymous reviewers for their helpful comments and suggestions. Author Contributions  ... 
doi:10.1371/journal.pone.0029903 pmid:22253821 pmcid:PMC3256230 fatcat:3bn34nd4prbn7fca3vbsty63qe

Sea lettuce systematics: lumping or splitting? [article]

Paulo Horta, Manuela Bernardes Batista, Regina L. Cunha, Rita Castilho
2018 bioRxiv   pre-print
Pervasive human-mediated gene flow through ballast water and widespread morphologic plasticity are the most likely explanations for the difficulty in establishing a reliable phylogenetic framework for  ...  Maximum likelihood, Bayesian analyses and species delimitation tests support the existence of 22 evolutionary significant units (ESUs), lumping the currently recognized number of species.  ...  These setting were used in the maximum 306 likelihood (ML) analysis that was performed with PhyML v3.0 [52].  ... 
doi:10.1101/413450 fatcat:6mtit35inrgu7nimfr5qoeefwi

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Federico Abascal, Rafael Zardoya, Maximilian J. Telford
2010 Nucleic Acids Research  
We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations.  ...  TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs  ...  Phylogenetic trees were inferred using the maximum likelihood-based software Phyml v3.0 (19) using the best-fit model GTR+I+G as identified by ModelTest (20) .  ... 
doi:10.1093/nar/gkq291 pmid:20435676 pmcid:PMC2896173 fatcat:ogyvyilhu5g3pc24ol6pihlqem

Page 293 of Genetics Vol. 178, Issue 1 [page]

2008 Genetics  
GascuEL, 2005 PHYML Online: a web server for fast maximum likelihood-based phyloge- netic inference. Nucleic Acids Res. 33: W557—W559. HALLMANN, A., and S.  ...  Iron, 1994 Phylogenetic relationships within the colonial Volvocales (Chlorophyta) inferred from cladistic analysis based on morphological data. J. Phycol. 30: 353-365. Nozakl, H., M. Iron, R.  ... 

PhEVER: a database for the global exploration of virus–host evolutionary relationships

Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, Christian Gautier
2010 Nucleic Acids Research  
Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains.  ...  This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers.  ...  maintenance of the PhEVER server.  ... 
doi:10.1093/nar/gkq1013 pmid:21081560 pmcid:PMC3013642 fatcat:swlnqhlp55abbnbybh5zoc5k4i

Applied aspects of methods to infer phylogenetic relationships amongst fungi

AJ Dissanayake
2020 Mycosphere  
This reference manuscript is originally conceived for usage with a set of programs necessary for inference of phylogenetic analyses in fungal research (taxonomy and phylogeny).  ...  There is a need to document the methodologies used for molecular phylogenetic analyses since the current fungal identification, classification and phylogeny are necessarily applied with DNA molecular sequence  ...  Samarakoon are thanked for their assistance on figure editing.  ... 
doi:10.5943/mycosphere/11/1/18 fatcat:gz6iinpo55debgebotua5idnam
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