A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is application/pdf.
Filters
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
2005
Nucleic Acids Research
Preserved Fulltext
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
2012
American Journal of Bioinformatics Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2010
BioTechniques
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2008
Systematic Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
, 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
2009
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2014
Msphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2019
PLoS Neglected Tropical Diseases
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2012
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2010
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
The Internet Archive has digitized a microfilm copy of this work. It may be possible to borrow a copy for reading.
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
2010
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2020
Mycosphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 233 results