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Protocols

Phylogeny.fr specifications

Information


Unique identifier OMICS_19276
Name Phylogeny.fr
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • BLAST-EXPLORER

Documentation


Maintainer


  • person_outline Guillaume Blanc

Publications for Phylogeny.fr

Phylogeny.fr citations

 (549)
library_books

A phylogenetic analysis of the Primnoidae (Anthozoa: Octocorallia: Calcaxonia) with analyses of character evolution and a key to the genera and subgenera

2018
BMC Evol Biol
PMCID: 5930830
PMID: 29716521
DOI: 10.1186/s12862-018-1182-5

[…] d rDNA locus was aligned using MAFFT v7.309 [, ]. The final alignment was 2831 bp – mtMutS: 828 bp, COI: 675 bp, 28S:600bp, and 18S: 728 bp (Additional file ). Gblocks v0.91b [], utilized through the Phylogeny.fr sever [], was used to remove ambiguous regions of each 18S and 28S alignment. Gblocks options were set to allow less stringent flanking regions and gap positions, and the resulting parame […]

library_books

The Hydrophobin Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis

2018
Front Plant Sci
PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] (MUltiple Sequence Comparison by Log-Expectation; Gap Open penalty−2, Edgar, ) tool implemented in MEGA7 (Tamura et al., ). Maximum likelihood analysis (Guindon and Gascuel, ) was conducted using www.phylogeny.fr in advanced mode (Dereeper et al., ). The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (v3.1/3.0 aLRT).Bioinformatic analyses o […]

library_books

Glycosylation of Hemagglutinin and Neuraminidase of Influenza A Virus as Signature for Ecological Spillover and Adaptation among Influenza Reservoirs

2018
Viruses
PMCID: 5923477
PMID: 29642453
DOI: 10.3390/v10040183

[…] Phylogenetic trees were constructed using Methods and Algorithms for Bioinformatics (MAB) phylogeny.fr analysis [,]. Amino acid sequences of the classical swine viruses from the the early 1930s, 1976, and the early 1990s [] as well as human isolates were collected in FASTA format from NCBI […]

call_split

Quantification of pathogenic Leptospira in the soils of a Brazilian urban slum

2018
PLoS Negl Trop Dis
PMCID: 5906024
PMID: 29624576
DOI: 10.1371/journal.pntd.0006415
call_split See protocol

[…] Edit 7.2.0 (Ibis Biosciences), and the sequences compared using BLAST to those available in the NCBI. In addition, we performed a phylogenetic analysis for the lipl32 and 16S rRNA amplicons using the Phylogeny.fr platform []. Maximum Likelihood trees were inferred by PhyML 3.0 [] using the Hasegawa-Kishono-Yano (HKY85) substitution model and 1000 bootstrap replicates. We used FigTree v1.4.2 (http: […]

library_books

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7 kb Geobacillus stearothermophilus bacteriophage TP 84 and its classification in the new Tp84virus genus

2018
PLoS One
PMCID: 5889276
PMID: 29624616
DOI: 10.1371/journal.pone.0195449

[…] ng ARNold [].Homologs of the large subunit terminase (TerL) and thymidylate synthase (Ts) proteins were identified using BLASTP and Newick formatted trees were generated using the "One click" mode at phylogeny.fr []. The data was then massaged using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). […]

library_books

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

2018
Nucleic Acids Res
PMCID: 5934628
PMID: 29660015
DOI: 10.1093/nar/gky256

[…] raphics System, Version 1.7 Schrödinger, LLC). Electrostatic potential surfaces were generated using the ‘APBS Tools’ plugin in PyMOL. Phylogenetic trees of the aligned sequences were generated using phylogeny.fr (). […]


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Phylogeny.fr institution(s)
Information Génomique & Structurale - CNRS-UPR2589, Institut de Microbiologie de la Méditerranée - IFR 88, Marseille, France
Phylogeny.fr funding source(s)
Supported by fundings from the ‘Réseau National des Génopoles’ (RNG), “Infrastructures en Biologie Santé et Agronomie” (GISIBISA) and CNRS.

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