Tuesday, November 7, 2017

PhyloNetworks: a package for phylogenetic networks

Recently, another computer package was released that is of relevance to this blog. This is described in a forthcoming paper:
Claudia Solís-Lemus, Paul Bastide, Cécile Ané (2017) PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution (in press).
The authors describe the package this way:
PhyloNetworks is a Julia package for the inference, manipulation, visualization and use of phylogenetic networks in an interactive environment. Inference of phylogenetic networks is done with maximum pseudolikelihood from gene trees or multi-locus sequences (SNaQ), with possible bootstrap analysis. PhyloNetworks is the first software providing tools to summarize a set of networks (from a bootstrap or posterior sample) with measures of tree edge support, hybrid edge support, and hybrid node support. Networks can be used for phylogenetic comparative analysis of continuous traits, to estimate ancestral states or do a phylogenetic regression.

The  SNaQ analysis is described in a previous paper:
Solís-Lemus C, Ané C (2016) Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLOS Genetics 12:e 1005896.
The phylogenetic model used incorporates: mutations (as usual), incomplete lineage sorting of alleles in ancestral populations (using the coalescent), and horizontal inheritance of genes (ie. reticulations in the network). The likelihood is decomposed into quartets, which makes the likelihood calculations relatively fast, and also allows the analyses to be scaled up to many species and many genes.

The PhyloNetworks software is open source, and is available with documentation at:
Have fun learning to use the Julia system, which I had never even heard of before investigating this new package!

Note: In spite of the similarity in name, this new package has nothing to do with Luay Nakhleh's PhyloNet package, nor to the Phylogenetic Networks blog.

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