PhyleasProg protocols

View PhyleasProg computational protocol

PhyleasProg statistics

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Associated diseases

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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 in pipelines

 (2)
2015
PMCID: 4453067
PMID: 25912043
DOI: 10.1093/gbe/evv072

[…] 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 […]

2015
PMCID: 4453067
PMID: 25912043
DOI: 10.1093/gbe/evv072

[…] conversion events. the figure for gene conversion events detected with the g0 option was made using circos ()., the inference of positive selection was performed on the tree of paralogous genes by phyleasprog with branch-site and site models of codeml of the paml package, with the fast option (). the multiple sequence alignment was carefully examined to avoid all false positive results. […]


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PhyleasProg in publications

 (4)
PMCID: 4592010
PMID: 26431526
DOI: 10.1371/journal.pone.0139517

[…] 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. […]

PMCID: 4453067
PMID: 25912043
DOI: 10.1093/gbe/evv072

[…] genome with 24 out to 26 paralogs involved in at least one recent gene conversion ( and supplementary data s9, supplementary material online). moreover, by using the site models implemented in phyleasprog, which allows the ω ratio to vary among sites, we detected eight different positions under positive selection scattered along the sequence of the ffar2 paralogs. by using the branch-site […]

PMCID: 3797742
PMID: 24147118
DOI: 10.1371/journal.pone.0078199

[…] positive selection [-], we carried out positive selection analyses on bmp15. we used the bmp15 sequences from 24 mammals ( and ) analyzed by branch-site models from paml packages [] within the phyleasprog web server [], in order to determine whether the different species of the phylogenetic tree underwent selective pressures and to detect signals of local episodic positive selection. […]

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

[…] the proteins present in the cluster 4, found in the above analysis to be significantly enriched for probesets annotated as immunity-related genes. a set of 251 proteins was analyzed with the phyleasprog web server [], and a subset of 242 proteins having at least 10 orthologs and being compatible with threshold of statistical significance was included in final analyses., among these 242 […]


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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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