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PhyloNet-HMM specifications


Unique identifier OMICS_10317
Name PhyloNet-HMM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes


No version available


  • person_outline Luay khleh

Publication for PhyloNet-HMM

PhyloNet-HMM citations


A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

BMC Bioinformatics
PMCID: 5064893
PMID: 27737628
DOI: 10.1186/s12859-016-1277-1

[…] ation genetic quantities (e.g., the CoalHMM method [] which utilizes a hidden Markov model (HMM) to capture within-genome sequence dependence), and detecting genomic loci involved in gene flow (e.g., PhyloNet-HMM []). We note that these inference problems are contained within the general phylogenetic inference problem. Since the primary focus of our study is the general phylogenetic network infere […]


Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent based approach

BMC Genomics
PMCID: 4895787
PMID: 26819241
DOI: 10.1186/s12864-015-2298-2

[…] odologies have been proposed to perform phylogenomic inference under models that explicitly incorporate the complex interplay of these different evolutionary processes [–]. Of particular relevance is PhyloNet-HMM [], a method that we collaboratively developed. PhyloNet-HMM is the first method capable of scalable phylogenomic inference on three or more genomes under a model that includes these evol […]

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PhyloNet-HMM institution(s)
Department of Computer Science, Rice University, Houston, TX, USA; Department of Ecology and Evolutionary Biology, Rice University, Houston, TX, USA

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