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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

[…] of genomic location during the evolution of the brassicaceae. to this end, we first identified blocks of synteny by comparing each modern genome to the ancestral brassicaceae genome using phyldiag []. in keeping with the high degree of conservation of genome organization among the brassicaceae [, ], a large fraction of the descendants of the 27,343 protogenes could be assigned […]

library_books

High precision detection of conserved segments from synteny blocks

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

[…] identifies mono-genic conserved segments, the third returns non-overlapping segments and the fourth repairs incorrect ruptures of synteny. all these refinements are implemented in a new version of phyldiag that has been benchmarked against i-adhore 3.0 and cyntenator, based on a realistic simulated evolution and true simulated conserved segments., the pre- and post-processing steps […]


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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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