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Protocols

PhyleasProg specifications

Information


Unique identifier OMICS_15385
Name PhyleasProg
Interface Web user interface
Restrictions to use None
Input data A list of Ensembl protein IDs and a list of species.
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Géraldine Pascal

Publication for PhyleasProg

PhyleasProg citations

 (6)
library_books

LMAP: Lightweight Multigene Analyses in PAML

2016
BMC Bioinformatics
PMCID: 5011788
PMID: 27597435
DOI: 10.1186/s12859-016-1204-5

[…] wo or more CPUs, thus providing a reasonable amount of processing capacity.In addition to the desktop-based applications described, there are also web-server implementations available, namely PSP [], PhyleasProg [] and Selecton version 2.2 []. All involve SM, but PSP and PhyleasProg also include BSM analyses.To our knowledge, from the available literature and from the mentioned multi-task software […]

call_split

Phylogenesis and Biological Characterization of a New Glucose Transporter in the Chicken (Gallus gallus), GLUT12

2015
PLoS One
PMCID: 4592010
PMID: 26431526
DOI: 10.1371/journal.pone.0139517
call_split See protocol

[…] ships between different species were carried out by combining the phylogenetic reconstruction of the gene family with the syntenic comparison. The GLUT12 proteins identified were then analysed by the PhyleasProg web server (Phylogenetic Analysis Programs v2.7 []) with fine computation and results on orthologs and paralogs. The phylogenetic tree of the SLC2A12 gene was displayed by Archaeopteryx. S […]

library_books

Expanding Duplication of Free Fatty Acid Receptor 2 (GPR43) Genes in the Chicken Genome

2015
Genome Biol Evol
PMCID: 4453067
PMID: 25912043
DOI: 10.1093/gbe/evv072

[…] ECONV version 1.81 (), which is a well-established method for detecting partial gene conversion (). The analysis was performed on the codon-based alignment performed by the Muscle algorithm () in the PhyleasProg pipeline () and permitted to the program to look for pair of sequences which are sufficiently similar to be suggestive of nonreciprocal transfer of genetic information between the differen […]

call_split

Positive Selection in Bone Morphogenetic Protein 15 Targets a Natural Mutation Associated with Primary Ovarian Insufficiency in Human

2013
PLoS One
PMCID: 3797742
PMID: 24147118
DOI: 10.1371/journal.pone.0078199
call_split See protocol

[…] ensus cleavage site –RXXR- to the C-terminus) and on full coding sequence. Multiple sequence alignment (MSA), tree reconstruction as well as positive selection calculation are then computed using the PhyleasProg web server v3.0 with the “fine” and “orthologs only” options []. The PhyleasProg web server uses the codeml program from the PAML package [] to evaluate the ratio ω (ratio of non-synonymou […]

library_books

Structural and functional annotation of the porcine immunome

2013
BMC Genomics
PMCID: 3658956
PMID: 23676093
DOI: 10.1186/1471-2164-14-332

[…] hese proteins result from alternative splicing; to maximize comparisons, we retained only the longest protein. Thus, a subset of 251 proteins was studied for evidence of positive selection, using the PhyleasProg phylogenetic analysis web server (http://phyleasprog.inra.fr/; []). Based on Ensembl release 67, PhyleasProg enables users to reconstruct phylogenetic trees, calculate positive selection w […]

library_books

Evolution of Genes Involved in Gamete Interaction: Evidence for Positive Selection, Duplications and Losses in Vertebrates

2012
PLoS One
PMCID: 3434135
PMID: 22957080
DOI: 10.1371/journal.pone.0044548

[…] We have also submitted the protein sequence to the PhyleasProg web server (http://phyleasprog.inra.fr/) to determine selective pressures that shape the evolution of these genes and used a new phylogenetically-informed test to compare the amount of po […]

Citations

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PhyleasProg institution(s)
INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France; CNRS, UMR6175, Nouzilly, France; Université François Rabelais de Tours, Tours, France; IFCE, Nouzilly, France; INRA, SIGENAE, UR83 Recherches Avicoles, Nouzilly, France
PhyleasProg funding source(s)
Supported by MENRT PhD fellowship.

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