Phylogeny Programs. Here are 392 phylogeny packages and 54 free web servers, (almost) all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly monthly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines. The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses. ... by methods available ... by computer systems on which they work ... cross-referenced by method and by computer system. ... by ones which analyze particular kinds of data.
PAUP* 4.0. Phylogenetic Analysis by Maximum Likelihood (PAML) Ziheng Yang Table of contents Introduction PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
This document is about downloading and compiling PAML and getting started. Downloading and Setting up PAML PAML-X: A GUI for PAML A graphical user interface, called PAML-X, has been written by Bo Xu of Institute of Zoology, Chinese Academy of Sciences in Beijing. The following is written for the naive user. PAML for Windows 9x/NT/2000/XP/Vista/7 Setting up a folder of local programs and changing the search path. Tar xzf paml4.7a.tgz. Laboratoire d'Informatique Robotique Microélectronique de Montpe. MEGA - Molecular Evolutionary Genetics Analysis. TREE-PUZZLE. Homepage. Start [HyPhy] PHYLIP Home Page. Phylo_win. NJplot. NEW: NJplot plots trees in PDF and PostScript formats (not for MacOS). NEW: NJplot allows to open several tree windows. NEW: NJplot can draw multibranched trees with or without branch lengths. NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).
NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. A screen shot of the main window of njplot is available here. Use of NJPlot Any rooting of the unrooted tree can be interactively specified using the mouse. Download NJplot Executables and full source code can be downloaded through our FTP server. The Mac and Windows versions are self-extracting archives which include an example file, help information, and the unrooted program that draws unrooted trees. For unix versions, get also an example tree file and the on-line help file. Reference. MrBayes: Home. .: Steven M. Vamosi :.