Table of Contents0 Changes since version 3.13Incompatible changes and added featuresBug fixes and minor corrections1 Introduction2 Getting startedWindows 95/98NT/2000/XP and UNIX (including Mac OS X)MACs3 Files in the PackageExample data setsWhich files are needed?4 Input File FormatsSequence data formatTree file format and representations of tree topologybaseml control filebasemlg control filecodeml (codonml and aaml) control fileCodon sequences (seqtype = 1)Amino acid sequences (seqtype = 2)evolveryn00mcmctree5 Models and MethodsNucleotide Substitution ModelsTransition/transversion rate ratioVariable rates among sitesCodon Substitution ModelsThe Basic ModelThe Branch ModelsThe Site ModelsBranch-site modelThe clade modelAmino Acid Substitution ModelsModels for combined analyses of partitioned dataFor nucleotides (baseml)For codons (codeml with seqtype = 1)For amino acids (codeml with seqtype = 2)Global and local clocks, and dated sequencesReconstruction of ancestral sequencesAnalysing large data sets and iteration algorithmsTree search algorithmsSimulation6 Seldom used featuresInputting site pattern frequencies (baseml/codeml)More codon modelsAnother pair of NSsites models for detecting positive selectHow to bootstrap?7 Technical NotesThe rub file recording the progress of iterationHow to specify initial valuesFine-tuning the iteration algorithmAdjustable variables in the source codes9 ReferencesIndexUser’s Guide PAML: Phylogenetic Analysis by Maximum Likelihood Version 3.14 (September 2004) Ziheng Yang1 © Copyright 1993 – 2004 by Ziheng Yang. The software package is provided "as is" without warranty of any kind. In no event shall the author or his employer be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The program package, including source codes, example data sets, executables, and this documentation, is distributed free of charge for academic use only. Permission is granted to copy and use programs in the package provided no fee is charged for it and provided that this copyright notice is not removed. Suggested citation: Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood Computer Applications in BioSciences 13:555-556 (http://abacus.gene.ucl.ac.uk/software/paml.html). The author can be reached at Ziheng Yang Department of Biology University College London Gower Street London WC1E 6BT, England Phone: +44 (20) 7679 4379 Fax: +44 (20) 7679 70962 Table of Contents 0 Changes since version 3.13...........................................................................................................3 Incompatible changes and added features......................................................................................3 Bug fixes and minor corrections.....................................................................................................4 1 Introduction...................................................................................................................................6 2 Getting started...............................................................................................................................7 Windows 95/98NT/2000/XP and UNIX (including Mac OS X).......................................................7 MACs ..............................................................................................................................................8 3 Files in the Package.......................................................................................................................8 Example data sets ...........................................................................................................................9 Which files are needed?................................................................................................................10 4 Input File Formats......................................................................................................................10 Sequence data format....................................................................................................................10 Tree file format and representations of tree topology...................................................................13 baseml control file .....................................................................................................................14 basemlg control file...................................................................................................................19 codeml (codonml and aaml) control file................................................................................19 Codon sequences (seqtype = 1)............................................................................................20 Amino acid sequences (seqtype = 2)....................................................................................22 evolver......................................................................................................................................23 yn00.............................................................................................................................................24 mcmctree ...................................................................................................................................24 5 Models and Methods...................................................................................................................25 Nucleotide Substitution Models ....................................................................................................25 Transition/transversion rate ratio ..............................................................................................26 Variable rates among sites ........................................................................................................27 Codon Substitution Models...........................................................................................................27 The Basic Model.......................................................................................................................27 The Branch Models...................................................................................................................28 The Site