CONSEL: for assessing the confidence of phylogenetic tree selection
WHAT IS CONSEL?
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique. This newly developed method gives less biased results than the conventional methods.
QUICK GUIDE:Using CONSEL is Easy! (updated 2008/09/12 for PAUP; 2010/01/30 for PhyML)
The computer software CONSEL and the theory behind it are described in the following papers. For the use of CONSEL, Shimodaira & Hasegawa (2001) may be referenced.
Shimodaira, H. An application of multiple comparison techniques to model selection. Ann. Inst. Statist. Math.50, 1-13 (1998).
Shimodaira, H. Multiple comparisons of log-likelihoods and combining nonnested models with applications to phylogenetic tree selection. Comm. in Statist., Part A - Theory Meth.30, 1751-1772 (2001).
Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol.,51, 492-508 (2002).
Shimodaira, H. & Hasegawa, M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol.16, 1114-1116 (1999).
Shimodaira, H. & Hasegawa, M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics17, 1246-1247 (2001).
Shimodaira, H. (2004) "Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling," Annals of Statistics, 32, 2616-2641.
Shimodaira, H. (2008) "Testing Regions with Nonsmooth Boundaries via Multiscale Bootstrap," Journal of Statistical Planning and Inference, 138, 1227-1241. http://dx.doi.org/10.1016/j.jspi.2007.04.001
Shimodaira, H. (2006-2008) "scaleboot: Approximately Unbiased P-values via Multiscale Bootstrap" http://cran.r-project.org/web/packages/scaleboot/index.html
consel01j.zip (DOS-BINARY, documents, examples)
: 2010/01/18 Tristan Gross and Silvia E. Smith complied this version for Windows. The Makefile was modified to work with the mingw cross compiler. The binary executables are in bin directory. I appreciate their help.