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PAML (for Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3.
Before running any of the programs included in the PAML software, please go through the different sections of this Wiki, where a detailed explanation of how to install and run the programs is given. One of the main problems users face is related to data formatting. In that way, please make sure that you go through the section Data formatting
before running any PAML program and format your input and control files accordingly.
If you have any questions, please first read the FAQs document as they might be answered in this document. If not, please use the search tool in the PAML discussion group to check whether your question/s have already been asked by other PAML users. If you still cannot find an answer to your questions, please post them in the PAML discussion group.
ANSI C source codes and executable files are distributed for UNIX, Linux, and Mac OS X (see the latest stable release available on this GitHub repository). PAML is not good for tree making, although it may be used to estimate parameters and test hypotheses to study the evolutionary process once you have reconstructed trees using other programs such as RAxML-NG
, IQ-TREE
, PAUP*
, PHYLIP
, PhyML
, etc.
To download and install PAML software, please follow the next links in the wiki:
- Overview
- Data file formats
If you use PAML, please cite the following:
- Yang, Z (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
- Yang, Z (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591.
If you use the PAML program MCMCtree
, please cite the following papers if you have used/run...
- ... the approximate likelihood calculation to speed up analyses with phylogenomic datasets (calculating Hessian and gradient):
- ... Bayesian model selection analysis for relaxed-clock models:
- ... the models for continuous morphological characters implemented in
MCMCtree
: - ... the protocol Bayesian Molecular Clock Dating Using Genome-Scale Datasets:
-
dos Reis M and Yang, Z (2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 1910. Humana, New York, NY. You can also access this chapter and the code used throughout the protocol on the
divtime
GitHub repository maintained by Mario dos Reis.
-
dos Reis M and Yang, Z (2019). Bayesian Molecular Clock Dating Using Genome-Scale Datasets. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 1910. Humana, New York, NY. You can also access this chapter and the code used throughout the protocol on the
- ... the protocol Environmental Microbial Evolution: Methods and Protocols:
- ... the sequential-subtree approach and/or fitting skew-t distributions to fossil calibrations:
If you use the PAML program CODEML
, please cite the following papers if you have used/run...
- ... the protocol A Beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome:
- ... the protocol Beginner's guide on the use of PAML to detect positive selection and/or the corresponding GitHub tutorial on the
positive-selection
repository:- Álvarez-Carretero S, Kapli P, Yang Z (2023). Beginner's guide on the use of PAML to detect positive selection, Mol Biol Evol, 40(4):msad041.. Remember to read the supplementary material where we discuss (i) analyses and checks you should carry out before running tests of positive selection with CODEML, (ii) gene tree VS species tree, and (iii) the usage of rooted and unrooted trees.
Recent changes and bug fixes are documented in the file doc/pamlHistory.txt.
Please post your questions and comments at the google discussion site for PAML. Please only raise issues on this GitHub repository when you experience any technical problems.
© Copyright 1993-2023 by Ziheng Yang
The software package is provided "as is" without warranty of any kind. In no event shall the author or their 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 maintained by Ziheng Yang and distributed under the GNU GPL v3.
Ziheng Yang
Department of Genetics, Evolution, and Environment
University College London
Gower Street
WC1E 6BT, London, United Kingdom