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Phylogenetic Analysis by Maximum Likelihood (PAML)
Phylogenetic Analysis by Maximum Likelihood (PAML)
Ziheng Yang
Table of contents
Introduction
How fast is my new computer? Get the benchmark and save it as speed2.tar.gz!!!
Downloading and setting up PAML
Some notes about running programs in PAML
To ask questions, go to The PAML discussion site. Old posts are at Genetics
Software Forum
PAML Manual (pamlDOC.pdf)
PAML FAQs (pamlFAQs.pdf)
Old versions of paml
PAML Resources on the web
PAML demo by Joe Bielawski for book chapter by Bielawski & Yang, 2005
Questions and Bug Reports
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. See the manual (pamlDOC.pdf) for
more information about running programs in the package.
Downloading and Setting up PAML
This section is written for the naive user. If you know things like
folders, executable files, and search path, there is no need for you
to follow the instructions here.
Windows 9x/NT/2000/XP/Vista
Download and save, on your local disk, paml4.2a.tar.gz (use the name paml4.2a.tar.gz, not paml4.2a.tar.tar, as
Internet Explorer may want you to use). Unpack the archive into a
folder, using Winzip, say. Remember the name of the folder. The
Windows executables are in paml42/bin/. I suggest that you create a folder for local
prorams and move the PAML executables there.
Setting up a folder of local programs and change the search path. You need to do this for your user account only once.
Suppose your user folder is C:\Users\Ziheng. [Please replace this with your own user folder in the following examples.]
This is the default user folder for me on Vista. On Windows XP, it is more unwieldly, somthing like
C:\Documents and Settings\Ziheng. Use Windows Explorer to create a folder called bin inside your user folder,
that is, C:\Users\Ziheng\bin. Or if you are the boss of your PC, you may prefer the folder C:\bin.
Anyway, this is the folder for holding executable programs.
Next we will add this folder onto the search path, which the OS uses to search for executable programs.
The following is for Windows Vista. The menu may be slightly different on Win 2000/XP, but you should have
no problem finding your way. Open Control Panel. Choose Classic View. Double-click on System.
Choose Advanced System Settings, and click on the tab Advanced. Click on the button Environment Variables.
Under User variables, double-click on the variable Path to edit. Click on the "variable value" field
and move the cursor to the beginning. Insert the name of our program folder C:\Users\Ziheng\Bin;
or C:\Bin; or whatever folder you have created. Note that the semicolon separates the folder names.
Be careful not to introduce any errors. Click on OK.
Copy the PAML executables. Copy or move the pre-compiled
executables (baseml.exe, codeml.exe, evolver.exe, chi2.exe, etc.)
from the paml42\bin\ folder to the local programs folder
C:\Users\Ziheng\Bin\. After this, you can execute any of these
programs from a command prompt whever you are. If you like, you can
rename baseml.exe and codeml.exe as baseml4.exe and codeml4.exe
respectively, to include the version number. (You will then run the
program by the command codeml4 instead of codeml.)
You can also copy other command-line programs you downloaded into
this folder, such as mb and the phylip programs.
Running a PAML program. Avoid double-clicking the program
names from Windows Explorer. That way you won't see any error
messages on the screen when the program crashes. Instead start a
"command prompt" box. For example, Start - Programs - Accessories -
Command Prompt). Or Start - Run - type cmd and OK. You can
right-click on the title bar and choose Properties to change the size,
font, colour of the window. cd to the folder which contains your user
files, and type the command name. Here we cd to the paml folder
(suppose you have extracted the archive into C:\Programs\paml42\) and
run program using the default files.
C:
cd \Programs\paml42\
codeml
Because there is no executable file called codeml.exe (or
codeml.bat, etc.) in your current folder, the OS will look for it in
the folders listed in the environment variable path. It will find and
execute codeml.exe in the C:\Users\Ziheng\Bin folder. You can also
specify the full path of the exectuable program, with something like
the following:
C:\Programs\paml42\bin\codeml
Some codeml analyses use an amino acid distance (e.g.,
grantham.dat) or substitution rate matrice (e.g., wag.dat). You will
then need to copy the necessary file to your current folder.
Otherwise the program will ask you to input the full path-name for the
file.
UNIX/Linux
and Mac OSX
MAC OSX. Download the Windows archive. Open a command
terminal (Applications-Utilities-Terminal) and compile and run the
programs from the terminal. Remove the .exe files in the bin/ folder.
Follow the instructions below for UNIX.
UNIX, linux, and other systems. Download the the Win32
archive and save and unpack it into a local folder. Remove the
Windows executables (.exe files) in the bin/ folder. (Replace 4.2
with the appropriate version number in the following commands.)
gzip -d paml4.2.tar.gz
tar xf paml4.2.tar
Then cd to the paml folder (you have to remember where you saved the
files) and again cd to the src/ folder and compile the programs.
rm bin/*.exe
cd src
make -f Makefile
ls -lF
rm *.o
mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin
cd ..
ls -lF bin
bin/baseml
bin/codeml
bin/evolver
Note for Mac OSX. If you get a "Command not found" error when you type commands gcc or make,
you may not have installed the C compiler correctly. You have to ownload the
Apple Developer's Toolkit at the Apple web site
http://developer.apple.com/tools/.
You may have to open and edit the file Makefile before compiling using make. For example, you can
change cc to gcc and -fast to -O3 or -O4. Also see readme.txt in the same folder for compiling
instructions. You might want to mv the executables into the bin/ folder on your accounts rather
than the paml main folder. And finally, if your current folder is not on your search path, you will
have to add ./ in front of the executable file name; that is, use
./codeml instead of codeml to run codeml. See below for details.
Setting up a folder of local programs and change your initialization file for the shell.
You need to do this for your user account only once. First check that there is a bin/ folder inside your account.
If not, create one.
cd
mkdir bin
Then modify your path to include the bin/ folder in the initialization file for the shell.
You can use more /etc/passwd to see which shell you run. Below are notes for the C shell and bash shell.
There are other shells, but these two are commonly used.
(1) If you see /bin/csh for your account in the /etc/passwd file, you are running the C shell,
and the intialization file is .cshrc in your root folder. You can use more .cshrc to see its content if it is present.
Use a text editor (such as emacs, vi, SimpleText, etc.) to edit (or create, if one does not exist) the file, by something like
emacs .cshrc
and insert the following line
set path = ($path . ~/bin)
The different fields are separated by spaces. Here '.' means the current folder,
and ~/ means your root folder, and ~/bin means the bin folder you created, and
$path is whatever folders are already in the path.
(2) If you see /bin/bash in the file /etc/passwd for your account, you are running the bash shell,
and the initialization file is .bashrc. Use a text editor to open .bashrc and insert the following line
PATH=$PATH:./:~/bin/
This changes the environment variable PATH. The different fields are separated by colon : and not space.
If the file does not exist, create one.
After you have changed and saved the initialization file, every
time you start a new shell, the path is automatically set for you.
You can then cd to the folder which contain your data files and run
paml programs there. The following moves to the paml folder (suppose
you have extracted the archive into Programs/paml42/ on your account)
and run program using the default files.
cd
cd Programs/paml42
codeml
As the path is set up properly, this is equivalent to
~/bin/codeml
Note that Windows uses \ while Unix uses /, and Windows is case-insensitive while Unix is case-sensitive.
Some notes about running programs in PAML
A number of example datasets are included in the package. They are typically datasets analyzed in
the original papers that described the methods. I suggest that you get a copy of the paper, and run the
example datasets to reproduce our results first, before analyzing your own data. This should serve to identify errors
in the program, help you to get familiar with the format of the data file and the
interpertation of results.
Most programs in the PAML package have control
files that specify the names of the sequence data file, the tree
structure file, and models and options for the analysis. The default
control files are baseml.ctl for baseml and
basemlg, codeml.ctl for codeml,
pamp.ctl for pamp, mcmctree.ctl
for mcmctree. The progam evolver does not
have a control file, and uses a simple user interface. All you do is
to type evolver and then choose the options. For other
programs, you should prepare a sequence data file and a tree structure
file, and modify the appropriate control files before running the
programs. The formats of those files are detailed in the documentation.
PAML Resources on the web
PAML discussion group (Old posts are at the Genetics Software Forum)
Redhat linux rpm in the Biorpms repository
ML estimation of dN and dS on the web
Joe Bielawski provided a PAML demo. See the data files and demo for the book chapter by Bielawski & Yang, 2005.
Linux Tutorial from Workshop on Molecular Evolution, Woods Hole
Questions and Bug Reports
(a) If you discover a bug, please post an item at
the discussion group or send me a message. I will try to visit the
discussion group every week or every two weeks. When describing the
problem, please mention the version number, what you did and what
happened. In particular copy any error message on the screen into
the message. Please try to make it easy for me to duplicate the
problem on my own computers. Please use an informative
"Subject:" field such as "paml/baseml: oom".
(b) If you have questions about using the programs, please try
to find answers by reading the manual (doc/pamlDOC.pdf), the paml
FAQ page (doc/pamlFAQ.pdf), or the postings at the discussion group
http://www.ucl.ac.uk/discussions/viewforum.php?f=54. (Old posts are at The GSF site).
Use example data files included in the package to get to know the
normal behavior of the programs. Often you should be able to tell
from the screen output whether the program reads the sequence and
tree files correctly.
If none of these is helpful, please post your question at the
discussion group, for me or other users of paml to answer. The
discussion group was set up to reduce the amount of time I have to
spend in answering user questions. Please do not send me messages.
I will most likely ignore emails asking questions about how to use
the programs. I apologize for the inadequate support.
Webmaster: Ziheng Yang
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