Phylogeny.fr protocols

View Phylogeny.fr computational protocol

Phylogeny.fr statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Phylogenetic inference chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 in pipelines

 (29)
2018
PMCID: 5889276
PMID: 29624616
DOI: 10.1371/journal.pone.0195449

[…] 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/)., the 468-bp cds, assigned as coding for ssb protein, was pcr amplified. for that purpose, two […]

2018
PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] sequences were further verified manually using the artemis. the phylogenetic trees for the amino acid sequences of the dna ligase, rnap, and capsid proteins were constructed using the service at phylogeny.fr []. the phylogenetic tree of the whole genome sequences were generated by victor []., the strategy to identify the physical ends of the genomes is outlined in . first, the phage dna […]

2017
PMCID: 5286464
PMID: 28197340
DOI: 10.1155/2017/8340746

[…] to multiple sequence alignment using bioedit software version 7.2.5 []. newick format was withdrawn from clustalw (http://www.ebi.ac.uk/tools/msa/clustalw2) [] to create a phylogenetic tree in phylogeny.fr software []., the nucleotide sequences of the rrs genes containing novel mutations were deposited in the genbank database (national center for biotechnology information; […]

2017
PMCID: 5322194
PMID: 28280489
DOI: 10.3389/fmicb.2017.00270

[…] for multiple sequence alignment, clustalw (larkin et al., ) (version 2.1) was used with default parameters. the phylogenetic tree was plotted with treedyn (chevenet et al., ) (version 198.3) on the phylogeny.fr server (dereeper et al., ) using default settings., rna extraction was performed using the mirneasy kit (qiagen). 500 ng of rna was applied to perform cdna synthesis using the miscript […]

2017
PMCID: 5384007
PMID: 28387353
DOI: 10.1038/srep46157

[…] plug-in in easyfig to reveal intercluster relationships. the phylogenetic analysis of homologous phage large terminase subunit or dna polymerase proteins was conducted in “one click” mode at phylogeny.fr (http://www.phylogeny.fr/). the trees were exported in netwick format and visualized using figtree (http://tree.bio.ed.ac.uk/software/figtree/)., mp1 and mp2 were isolated […]

Phylogeny.fr in publications

 (293)
PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] 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 […]

PMCID: 5923477
PMID: 29642453
DOI: 10.3390/v10040183

[…] agreement” among the nine networks [,], where a score of >0.5 is taken as a threshold for occupation., 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 […]

PMCID: 5906024
PMID: 29624576
DOI: 10.1371/journal.pntd.0006415

[…] 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 […]

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

[…] 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/)., the 468-bp cds, assigned as coding for ssb protein, was pcr amplified. for that purpose, two […]

PMCID: 5934628
PMID: 29660015
DOI: 10.1093/nar/gky256

[…] 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 ()., dna binding by wt val1-b3 was analyzed by the electrophoretic mobility shift assay (emsa) using 33p-labeled 12 bp oligoduplexes. 1 μm dna (2–4 nm of radiolabeled dna mixed with 1 μm […]

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