CONSEL: for assessing the confidence of phylogenetic tree selection

TLDR

Tree selection confidence is traditionally assessed by p‑values, but conventional methods such as BP, KH, SH, and WSH are biased; CONSEL offers a more accurate approach. The program aims to compute the AU test p‑value via a multi‑scale bootstrap technique. It derives AU, BP, KH, SH, and WSH p‑values from outputs of phylogeny packages like Molphy, PAML, and PAUP*, and can be applied to any problem where bootstrap probabilities are available. CONSEL is written in C and available for Unix and DOS at http://www.ism.ac.jp/~shimo/ (contact [e-mail]).

Abstract

Abstract Summary: CONSEL is a program to assess the confidence of the tree selection by giving the p-values for the trees. The main thrust of the program is to calculate the p-value of the Approximately Unbiased (AU) test using the multi-scale bootstrap technique. This p-value is less biased than the other conventional p-values such as the Bootstrap Probability (BP), the Kishino–Hasegawa (KH) test, the Shimodaira–Hasegawa (SH) test, and the Weighted Shimodaira–Hasegawa (WSH) test. CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available. Availability: The programs are written in C language. The source code for Unix and the executable binary for DOS are found at http://www.ism.ac.jp/~shimo/ Contact: [e-mail]