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treeio: Phylogenetic data integration

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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. Information associated with taxon species/strains can be meta-data (e.g. isolation host, time and location, etc.), phenotypic or experimental data. These data as well as analysis finding may…
Original Post: treeio: Phylogenetic data integration