Phylogeny.fr statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Phylogeny.fr
info

Tool usage distribution map

This map represents all the scientific publications referring to Phylogeny.fr per scientific context
info info

Associated diseases

This word cloud represents Phylogeny.fr usage per disease context
info

Popular tool citations

chevron_left Phylogenetic inference chevron_right
Want to access the full stats & trends on this tool?

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 (). […]


Want to access the full list of citations?
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.

Phylogeny.fr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Phylogeny.fr