emapi.pl Version 1.0 (April 2004) o About this software emapi.pl is a program for estimation of the amino acid composition of ancestral sequences using EM from a sequence alignment and phylogenetic tree provided by the user. For details of the algorithm please see: Brooks, D.J., Fresco, J.R., and Singh, M. (2004) A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics. Please cite this paper if you use this program for your research. o Installing emapi.pl gunzip -c emapi.tar.gz | tar -xf - You should also read the following files: COPYING -- copyright notice, and information on the free software license LICENSE -- Full text of the GNU Public License, version 2 (see COPYING) o Getting started emapi.pl is fairly inflexible in dealing with the format of infiles, so please read the following details carefully. (See the sample alignment, tree and start_pi files for clarification of the formatting requirements.) Usage: emapi.pl where is a file containing an UNGAPPED alignment in phylip format, with sequential integers starting from 1 as taxon identifiers. (phylip is a free software package for phylogenetic analysis available from Joseph Felsenfeld, University of Washington.) is a file containing a phylogenetic tree in Newick format, with branch lengths indicated by INTEGERS (corresponding to PAM distances). options: --threshold : threshold for convergence (default = 0.0001) --start_pi : file to read in starting amino acid composition (default start_pi) --end_pi : file to output estimated ancestral amino acid composition (default end_pi) The order of amino acid frequencies in file 'start_pi' must be: A R N D C Q E G H I L K M F P S T W Y V and all should be entered on a single line. The directory named 'Jones' containing conditional substitution matrices from 1 to 300 (entitled mp_xxx.mat) must be present in the same directory with emapi.pl.