DupliPHY-ML specifications

Information


Unique identifier OMICS_09945
Name DupliPHY-ML
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ryan M. Ames

Information


Unique identifier OMICS_09945
Name DupliPHY-ML
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ryan M. Ames

Publications for DupliPHY-ML

DupliPHY-ML citations

 (2)
library_books

Amino acid transporter expansions associated with the evolution of obligate endosymbiosis in sap feeding insects (Hemiptera: sternorrhyncha)

2015
BMC Evol Biol
PMCID: 4374396
PMID: 25887093
DOI: 10.1186/s12862-015-0315-3

[…] s used to reconcile the gene trees of APC and AAAP families (obtained from Duncan et al. []) with the species phylogeny, assigning default values for costs of duplications (1.5) and losses (1.0); (2) DupliPhy-ML [] was run online with default parameters, and the best models were selected using the Akaike Information Criterion (AIC, Additional file : Table S3); and (3) CAFE v. 3.1 [,] was used to i […]

library_books

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

2014
PLoS One
PMCID: 4055711
PMID: 24921666
DOI: 10.1371/journal.pone.0099480

[…] A phyogenetic species tree is necessary to infer the evolutionary histories of gene families. DupliPHY-ML does not use gene trees to infer events but instead will infer gain and loss events on the species phylogeny. Here, we used a subset of the cladogram presented in to get the phylogenetic […]

DupliPHY-ML institution(s)
Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, UK
DupliPHY-ML funding source(s)
Biotechnology and Biological Sciences Research Council, UK

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