分子進化解析ソフトウエアパッケージの先駆けとして世界中で愛用され続けている、PHYLIP packageにおいて、25年以上もの間放置されていた、不具合の原因を突き止め修正したうえで、自動化へ向けた補強アドイン・プログラムとともに公開しました。

A modification of the PHYLIP program: A solution for the redundant cluster problem, and an implementation of an automatic bootstrapping on trees inferred from original data.
Makoto K. Shimada and Tsunetoshi Nishida
Molecular Phylogenetics and Evolution 109: 409-414. DOI:10.1016/j.ympev.2017.02.012

• We corrected a software bug of PHYLIP, the evolutionary study package with the longest history.
• The bug had been left for more than 25 years.
• This correction solves the redundancy in bootstrapping that cause incorrect inference of consensus tree.
• We build an add-on program of PHYLIP that infers a tree from original data with the bootstrap values.
• We build an bash script that enable automatic tree construction from unaligned sequence data.

Felsenstein’s PHYLIP package of molecular phylogeny tools has been used globally since 1980. The programs are receiving renewed attention because of their character-based user interface, which has the advantage of being scriptable for use with large-scale data studies based on super-computers or massively parallel computing clusters. However, occasionally we found, the PHYLIP Consense program output text file displays two or more divided bootstrap values for the same cluster in its result table, and when this happens the output Newick tree file incorrectly assigns only the last value to that cluster that disturbs correct estimation of a consensus tree. We ascertained the cause of this aberrant behavior in the bootstrapping calculation. Our rewrite of the Consense program source code outputs bootstrap values, without redundancy, in its result table, and a Newick tree file with appropriate, corresponding bootstrap values. Furthermore, we developed an add-on program and shell script, add_bootstrap.pl and fasta2tre_bs.bsh, to generate a Newick tree containing the topology and branch lengths inferred from the original data along with valid bootstrap values, and to actualize the automated inference of a phylogenetic tree containing the originally inferred topology and branch lengths with bootstrap values, from multiple unaligned sequences, respectively. These programs can be downloaded at: https://github.com/ShimadaMK/PHYLIP_enhance/.