PhylDiag specifications

Information


Unique identifier OMICS_11730
Name PhylDiag
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License CeCILL version 2.1, GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Hugues Roest Crollius

Publication for PhylDiag

PhylDiag citations

 (2)
library_books

Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2 mediated gene regulation

2017
Genome Biol
PMCID: 5663038
PMID: 29084582
DOI: 10.1186/s13059-017-1333-9

[…] Synteny blocks were determined using the PhylDiag software [] starting from two genomes and the corresponding gene homologies. PhylDiag allows for gene deletions to be considered as events that may break the synteny and also accounts for gen […]

library_books

High precision detection of conserved segments from synteny blocks

2017
PLoS One
PMCID: 5495381
PMID: 28671949
DOI: 10.1371/journal.pone.0180198

[…] The pre-processing step that collapses clusters of tandem duplicates and the four refinement steps have been implemented in a new version of PhylDiag [] benchmarked by simulations, showing substantial improvements. Using a realistic simulation of the evolution of gene order []() and the corresponding simulated conserved segments, we comput […]

PhylDiag institution(s)
Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France; CNRS, UMR 8197, Paris, France; Inserm, U1024, Paris, France; European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
PhylDiag funding source(s)
This work is funded by Centre National de la Recherche Scientifique (CNRS) and grants from the Agence Nationale de la Recherche (ANR) [Ancestrome Project ANR-10-BINF-01-03, ANR Blanc-PAGE ANR-2011- BSV6-00801].

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