treeio: Phylogenetic data integration

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Author: Guangchuang Yu

Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the de facto format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats. However, analysis results (tree + analysis findings) from widely used software packages in this field are not well supported. Some of them are extended from Newick and Nexus (e.g. RevBayes and BEAST outputs), while some of the others are just log files (e.g. r8s and PAML outputs). Parsing these output files is important for interpreting analysis findings.

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The treeio package is now published in Molecular Biology and Evolution!
Li-Gen Wang, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, Casey W Dunn, Bradley R Jones, Tyler Bradley, Huachen Zhu, Yi Guan, Yong Jiang, Guangchuang Yu, treeio : an R package for phylogenetic tree input and output with richly annotated and associated data, Molecular Biology and Evolution , , msz240,

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