CONSEL: a program for assessing the confidence of phylogenetic tree selection ============================================================================= CONSEL v0.20 Time-stamp: "2011-05-12 16:30:57 shimo" Hidetoshi Shimodaira CHANGE OF AFFILIATION ======================= Hidetoshi Shimodaira has moved to Department of Mathematical and Computing Sciences Tokyo Institute of Technology 2-12-1 Ookayama, Meguroku, Tokyo 152-8552, Japan shimo@is.titech.ac.jp http://www.is.titech.ac.jp/~shimo/ The former institution is The Institute of Statistical Mathematics 4-6-7 Minami-Azabu, Minatoku, Tokyo 106-8569, Japan shimo@ism.ac.jp http://www.ism.ac.jp/~shimo/ 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, 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. PORTABILITY ============= CONSEL has been developed on a debian Linux box. It should work on the other UNIX machines with gcc installed. It has been tested on * Linux / debian (2.2.19, 2.4.18) * SGI IRIX (6.5.6) * MS-DOS (Windows 98, 2000, XP) MS-DOS USER ============= For MS-DOS (Windows 98, 2000, XP) users, the executable binary of CONSEL is available. Please download "cnslb01.exe" for the self-extracting archive. Read the document "DOSUSER.txt" in it. UNIX USER ============= For UNIX users, the source file of CONSEL is available. Please download "cnsls01.tgz" for the tar-gzipped archive. Read the document "UNIXUSER.txt" in it. DOCUMENTATION =============== A tentative user's guide of CONSEL is available at the same directory as this "README.txt" file. The PDF file is "program.pdf" and its TeX file is "program.tex". CREDITS ========= The program CONSEL is written by Hidetoshi Shimodaira. The raw-data reading functions are written by Hiroshi Mine. Some other functions are borrowed from other packages and modified for CONSEL; Molphy (Jun Adachi): luinverse. Meschach library (David E. Stewart): v_sort, skipjunk, and several ideas on the design of input/output routines. MT19937 random number generator (Takuji Nishimura and Makoto Matsumoto) is now used. I would like to appreciate the following people for making CONSEL. Masami Hasegawa: for letting me know the biological issues. Hiroshi Mine: for technical advice on debian linux and Windows. Joe Felsenstein: brought me to the field of phylogeny. Brad Efron: for suggestions to develop the method of the AU test. and all the other people who helped me for the development of CONSEL. REFERENCE =========== (1) Hidetoshi Shimodaira (2000) "Another calculation of the p-value for the problem of regions using the scaled bootstrap resamplings," Technical Report No. 2000-35, Stanford University. (2) Hidetoshi Shimodaira (2002) "An approximately unbiased test of phylogenetic tree selection," Systematic Biology, 51, 492-508. (3) Hidetoshi Shimodaira and Masami Hasegawa (2001) "CONSEL: for assessing the confidence of phylogenetic tree selection," Bioinformatics, 17, 1246-1247. (4) Hidetoshi Shimodaira (2004) "Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling," Annals of Statistics, 32, 2616-2641. (5) Hidetoshi Shimodaira (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 (6) Hidetoshi Shimodaira (2006-2008) "scaleboot: Approximately Unbiased P-values via Multiscale Bootstrap" http://cran.r-project.org/web/packages/scaleboot/index.html The theory is described in the references (1), (2) and (4). Please make a citation to the reference (3) for the use of the program CONSEL. Recently a new theory which generalizes those for CONSEL is developed. This new theory is described in (5) and implemented in the R package of (6). Hidetoshi Shimodaira Department of Mathematical and Computing Sciences Tokyo Institute of Technology http://www.is.titech.ac.jp/~shimo/ ---------- This file is part of CONSEL. CONSEL is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. CONSEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with CONSEL; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA