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Phylogene specifications

Information


Unique identifier OMICS_08352
Name Phylogene
Interface Web user interface
Restrictions to use None
Input data Protein name, Protein sequence (FASTA)
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Yuval Tabach

Publication for Phylogene

Phylogene citations

 (5)
library_books

Oxalobacter formigenes associated host features and microbial community structures examined using the American Gut Project

2017
Microbiome
PMCID: 5571629
PMID: 28841836
DOI: 10.1186/s40168-017-0316-0

[…] nment by MUSCLE 3.8.1, (ii) alignment refinement by Gblock, (iii) maximum likelihood phylogeny analysis by PhyML, and (iv) tree rendering by TreeDyn [–]. For detailed methods and parameters, refer to phylogene.fr website documentation section 2.1 []. The sequence identity matrix (Additional file : Figure S2B) was calculated with (1 − dist)% by the dist.alignment function [] from the seqinr package […]

library_books

PrePhyloPro: phylogenetic profile based prediction of whole proteome linkages

2017
PeerJ
PMCID: 5578374
PMID: 28875072
DOI: 10.7717/peerj.3712

[…] g hubs connecting to more input proteins by using centrality measurements (degree and betweenness).Several online tools exist for phylogenetic profiling, for example STRING (version 10) using SVD (), PhyloGene using NPP (), and ProtPhylo using “Hamming” (). PrePhyloPro based on PPP is a complementary online tool for whole proteome linkage predictions. PrePhyloPro includes several visualization met […]

library_books

Identifying the Deleterious Effect of Rare LHX4 Allelic Variants, a Challenging Issue

2015
PLoS One
PMCID: 4425544
PMID: 25955177
DOI: 10.1371/journal.pone.0126648

[…] Alignment of amino acid sequences was performed with Clustal X (www.clustal.org) and Phylogene (acces.ens-lyon.fr/biotic/evolut/phylogene/accueil.htm) softwares. Poliphen 2 (http://genetics.bwh.harvard.edu/pph2), Predict SNP (http://loschmidt.chemi.muni.cz/predictsnp) and UMD-HTS (www […]

library_books

Existence of a Colonizing Staphylococcus aureus Strain Isolated in Diabetic Foot Ulcers

2015
PMCID: 4512213
PMID: 25901094
DOI: 10.2337/db15-0031

[…] s () were chosen for optical mapping. Optical maps were provided by OpGen (Gaithersburg, MD), prepared on the Argus Optical Mapping System as described previously (), and analyzed with the support of Phylogene (Bernis, France). The optical maps of the studied strains were then compared with the in silico restriction maps of 19 sequenced S. aureus isolates whose sequence genomes were available in G […]

library_books

IMGT, the international ImMunoGeneTics information system®: a standardized approach for immunogenetics and immunoinformatics

2005
Immunome Res
PMCID: 1312312
PMID: 16305737
DOI: 10.1186/1745-7580-1-3

[…] IMGT/PhyloGene[] is an easy to use tool for phylogenetic analysis of variable region (V-REGION) and constant domain (C-DOMAIN) sequences. This tool is particularly useful in developmental and comparative i […]

Citations

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Phylogene institution(s)
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, Boston, MA, USA; Department of Developmental Biology and Cancer Research, The Institute For Medical Research-Israel-Canada; The Hebrew University-Hadassah Medical School, Jerusalem, Israel
Phylogene funding source(s)
Hebrew University start-up funds

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