The best way of running the programs listed below is by using the command line. Here, you have some links to command line tutorials on different operating systems:
The BP&P program implements a series of Bayesian inference methods under the multispecies coalescent model with and without introgression. The analyses may include estimation of population size (theta’s) and species divergence times (tau’s), species tree estimation, species delimitation, and estimation of cross-species introgression intensity. We suggest that you get BP&P version 4 as it contains all the functionalities of version 3.4 but runs much faster and supports multiple threads. Also, the multispecies-coalescent-with-introgression (MSci) model is implemented in BP&P v4 only, and not in BP&P v3.4. The same control file works for both versions.
The source code, installation guidelines, and tutorial for the latest version of BP&P can be found in the links below:
BP&P version 4, GitHub repository for source code.BP&P version 4, manual.BP&P version 4, installation instructions.BP&P v3.4.The source code and tutorial for the previous BP&P v3.4 is available in the links below:
BP&P version 3, source code.BP&P version 3, source code and executables for Mac OS X 7 and later.bpp3.4a.tgz includes the source code for all platforms, as well as executables for Windows..gz when the download finishes, you should change it back to .tgz before double-clicking.bpp3.4.macosx.tgz (source code and executables for Mac OS X 7 and later).If you have questions about either BP&P v3.4 or BP&P v4, please post them at the BP&P google group site here. Before posting a question, however, please use the search tool in the google groups site to make sure that other users have not already asked your query.
BP&P replaces the old program MCMCcoal, which implements the Bayesian method of Rannala & Yang (2003) and Burgess & Yang (2008).
Bruce Rannala has written a BPP GUI. The executables are for Windows and Mac OS X. You can use this to prepare the BP&P control files, and also read in the species trees in the MCMC sample file, produced by either BP&P v3.4 or BP&P v4. Please download the GUI from Bruce’s group web site here.
If you are using BP&BP, please cite:
Also, please cite the following papers depending on the method you use:
Before running BP&P, please read the following tutorials:
Also, please read the 2015 tutorial on BP&P v3.4.
Mario dos Reis has written the bppr R package, which can use the BP&P output to do the following:
BP&P phylogeny to geological time: tutorial available here.BP&P: tutorial here.An introduction to the bppr R package can be read here.
The program 3s implements likelihood ratio tests to test for gene flow between two closely related species.
The latest release (Dalquen et al. 2017) includes several improvements over previous versions:
3s uses an asymmetric IM model with θ1 ≠ θ2 and M12 ≠ M21.3s can take advantage of multi-core architectures to speed up computation.The source code is available here.
You can use 3s as it is, without any additional libraries installed. Please use the following command (adapted to your system) to compile the source code:
gcc -O3 -o 3s 3s.c tools.c lfun3s.c -lm
Nevertheless, we recommend installing the GNU Scientific library (GSL) as this will speed up computation of P(t) significantly, even if you run the program on a single core. Once GSL is installed, you can compile 3s. There are three different commands you should run depending on how your system is set up:
No extra commands are needed to compile 3s after installing the GSL:
gcc -O3 -DUSE_GSL -o 3s 3s.c tools.c lfun3s.c -lm -lgsl -lgslcblas
You might have to specify the location of GSL using the -I and -L options:
gcc -O3 -DUSE_GSL -I/usr/local/include -L/usr/local/lib -o 3s 3s.c tools.c lfun3s.c -lm -lgsl -lgslcblas
If you want to run 3s on multiple cores, you can compile the software with OpenMP support:
gcc -O3 -DUSE_GSL -I/usr/local/include -L/usr/local/lib -o 3s -fopenmp 3s.c tools.c lfun3s.c -lm -lgsl -lgslcblas
The program 3s should work out-of-the-box on current Linux systems with the GNU tool chain. On Mac OS X and Windows, you may need a compiler with OpenMP support.
If you use 3s, please cite the following papers:
At the moment, there are no tutorials available for this software.
PAML 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. ANSI C source codes are distributed for UNIX, Linux, and Mac OS X. Executables are provided for Windows. 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.
Before running any of the programs included in the PAML software, please read the PAML manual in PDF format here, where a detailed explanation of how to run the programs is given. 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 here to check whether your questions 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 here.
For more details on how to install and run PAML programs, as well as for data formatting, please visit the PAML Wiki on the PAML GitHub repository for a more interactive documentation.
PAML for LinuxPAML GitHub repository here to download the latest version.Now, follow the commands below:
# Move to the cloned repository. Make sure you have cloned it in the correct
# location of your local disk.
cd paml
# If there are executable files for Windows, you may remove them.
rm bin/*.exe
# Move to the `src` directory to compile the software.
cd src
make -f Makefile
# List all the compiled programs that are part of PAML and
# remove unnecessary files.
ls -lF
rm *.o
# Create a `bin` directory, which you can then export to your PATH.
mkdir ../bin
# Move the compiled programs to `bin`.
mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
# Test that you can run some PAML programs such as BASEML, CODEML, or evolver.
bin/baseml
bin/codeml
bin/evolver
Now, you can either export the path to this bin directory or include the executable files in a general bin directory for all the software that you have on your local disk, e.g., ~/bin. Whatever you decide to do, please modify your path to include the folder with the PAML programs in the initialization file for the shell. You can use more /etc/passwd to see which shell you run. Below, you can find some notes for the C shell and bash shell. There are other shells, but these two are commonly used.
/bin/csh for your account in the /etc/passwd file, you are running the C shell, and the initialization 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 vim, emacs, nano, etc.) to edit (or create, if one does not exist) the file, by running something like this:
emacs .cshrc
Now, insert the following line:
# Please change <path_to_bin> with the path on your system.
set path = ($path . <path_to_bin>/bin)
The different fields are separated by spaces. Here, . means the current folder, and ~/ means your root folder, and $path is whatever folders are already in the path.
/bin/bash in the file /etc/passwd for your account, you are running the bash shell, and the initialization file is ~/.bashrc or ~/bash_profile (type ls -a ~ to see whether you have one or another in your home directory, ~).
Now, use a text editor to open file ~/.bashrc and insert the following line:
# Please change <path_to_bin> with the path on your sysyem.
export PATH=<path_to_bin>/bin:$PATH
The command above changes the environment variable PATH. The different fields are separated by colon :, without spaces. If the file does not exist, please create one (e.g., run touch ~/.bashrc on the terminal).
cd to the folder which contains your data files and run PAML programs there. If the path is properly set, you will be able to run any of the PAML programs by just typing the file name (e.g., unless you have modified the executable file names, mcmctree, codeml, etc.).PAML for Mac OS XMac OS X with M1/M2/M3 chips: if you have one of the new macOS, you may be experiencing some issues (e.g., segmentation fault, trace trap) when running either the pre-compiled binaries from the latest release or your own compiled binaries using the corresponding source code. Linux/Windows binaries seem to automatically initialise to 0 some values that are related to memory access. Nevertheless, arm64-based devices seem to initialise those values differently (or they are stricter) as they have risc processors. This issue is related to the use of strcpy(t,s);, which copies source string s to target string t, when s and t are the same string at the same address. The source code in the dev branch has been fixed to account for this issue, but not yet been merged as of 2024/08/23. If you have one of the latest macOS and experience this issue, please do the following:
dev branch in the PAML GitHub repository.<> Code, which will download the source code in the dev branch. At the end of the download, you should see a zip file called paml-dev.zip saved in the directory you specified. # Move to the cloned repository.
cd paml-dev
# If there are executable files for Windows, you may remove them.
rm bin/*.exe
# Move to the `src` directory to compile the software.
cd src
make -f Makefile
# List all the compiled programs that are part of PAML and
# remove unnecessary files.
ls -lF
rm *.o
# Create a `bin` directory, which you can then export to your PATH.
mkdir ../bin
# Move the compiled programs to `bin`.
mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
# Test that you can run some PAML programs such as BASEML, CODEML, or evolver.
bin/baseml
bin/codeml
bin/evolver
NOTE
If you want to clone the repository from the terminal, make sure that you usegit checkoutto change branches!
dev branch).Some macOS users may have ~/.profile instead of ~/.bashrc as Linux users (see above). In that case, follow the same instructions as above but replace all ~/.bashrc with ~/.profile. If you have the Z shell and, perhaps, file ~/.zshrc, you can follow the recommendations given below based on the procedure that has proved successful for some PAML users:
Type ls -a ~ in “tab 1”. If you do not see a file called ~/.profile listed, then you will need to create it. You can then type touch ~/.profile. This will be the file that you will use to export the programs to the global path. E.g., you could open it with your preferred text editor and type :
# Please change <path_to_bin> with the path on your sysyem.
export PATH=<path_to_bin>/bin:$PATH
In “tab 1”, please check that you have a file called ~/.zshrc (i.e., ls -a ~). If not, please create one (i.e., touch ~/.zshrc), open it with your preferred text editor, and add this line:
[[ -e ~/.profile ]] && emulate sh -c 'source ~/.profile'
Now, save the file with your preferred text editor and source the changes (i.e., run first source ~/.profile, then source ~/.zshrc).
mcmctree, codeml, baseml; any of the programs that are part of PAML) which path you tried to export. If that works, then you have managed to export the path to PAML programs! If you experience any problems (e.g., commands such as cd or ls stopped working), then go back to the first terminal (i.e., terminal with “tab 1” where you modified files ~/.profile and ~/.zshrc) but, this time, go to “tab 2”, which you should have already opened before making any changes in “tab 1”. Now, we shall be able to recover the original files without changes (i.e., type source ~/.profile and source ~/.zshrc, which should not include the changes you made in “tab 1”). If you did not create them, just create empty ones (i.e., touch ~/.profile and touch ~/.zshrc) and source again. If you open a third terminal or a third tab, the problem should now be solved! Then, try again and make sure there are no typos in the path you type!PAML for Windows 10 or laterTo download the latest stable version of PAML, please go to the releases and download the compressed file that best suits your needs (i.e., pre-compiled binaries or source code for your operating system).
If you want to download the latest code available for PAML, you can clone the PAML GitHub repository here. You can download a zip compressed file to automatically start the download, and then decompress it on your local disk. Alternatively, you can use the command line:
# Open a terminal on the location where you want to save
# the PAML software.
git clone https://github.com/abacus-gene/paml.git
Now, you can use either the Windows Linux Subsystem, the Git Bash, or other alternatives to start a command-line shell that you may have installed on your PC to compile the PAML programs:
# Open a terminal where you have cloned the PAML repository
cd paml
cd src
make -f Makefile
# List all the compiled programs that are part of PAML and
# remove unnecessary files
ls -lF
rm *.o
# Create a `bin` directory, which you can then export to your PATH.
mkdir ../bin
# Move the compiled programs to `bin`
mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
If you export the PATH to the directory bin, you will be able to run the programs from any location of your local disk without needing to type the absolute path. Please note that, if you are a WSL users (i.e., you have the Windows Subsystem for Linux installed on your PC), your path will always start with mnt/c as the WSL is installed as a mountable disk. The easiest way to find the path to a program is to use a terminal to navigate to the directory where it was installed (i.e., use cd). Once you are there, type pwd. Then, you can use your favourite text editor to modify the ~/.bashrc as explained above for Linux users above.
The instructions below explain how to download older versions of PAML compatible with Mac OS X (G5 compiler) and Windows 9x/NT/2000/XP/Vista 7.
We have decided to keep this section in case users need to follow the installation steps for the OSs detailed above. Nevertheless, we discourage the installation of older versions as they are out of date. Users may follow the step-by-step installation/compilation guidelines below, but always using the latest version of the PAML software available here.
PAML versions for Mac OS XIMPORTANT
Please note that you should always download the latestPAMLversion from thePAMLGitHub repository. The notes below are for an earlier version,PAMLv4.8a.
A compiled version for Mac OS X of an older version of PAML can be downloaded from the following link: PAML v4.8a. If you have the latest latest versions of Mac OS X, please follow the instructions above to install PAML v4.8a – please note that it may not work due to software incompatibilities.
WARNING
Please use the instructions below only if you are trying to install an older version of PAML on older versions of Mac OS X. Please note that we always recommend to use the latest stable version ofPAML; these instructions are kept here for the record.
If you have a G5 or if you would like to compile the programs in the PAML software yourself, please follow the notes below.
We assume that the Apple XCODE is now automatically installed on your macOS. Otherwise, you will have to download and install the macOS XCODE system, which includes the C compiler. Without a C compiler, you will get a “Command not found” error when you type gcc or cc at the command terminal.
Applications > Utilities > Terminal)..exe files from the bin/ folder.Open up the file Makefile in the src/ folder and add # at the beginning of the following line to comment it out:
CFLAGS = -O4 -funroll-loops -fomit-frame-pointer -finline-functions
# at the beginning of the line for either G5 or intel, depending on your machine, to uncomment the line.For Mac OS X G5 uncomment the following line:
CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions
For Mac OS X intel uncomment the following line:
CFLAGS = -march=pentium-m -O4 -funroll-loops -fomit-frame-pointer -finline-functions
VERY IMPORTANT: Please save the file and compile after the programs are successfully compiled, delete the .o files and move the executables to the bin/ folder as follows:
rm *.o
mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin
You may 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 to run CODEML. See the notes for UNIX systems above.
PAML versions for Windows 9x/NT/2000/XP/Vista 7IMPORTANT
Please note that you should always download the latestPAMLversion from thePAMLGitHub repository. The notes below are for an earlier version,PAMLv4.9j. If you would like to use the latest stable version on Windows, you can either download the pre-compiled binaries or the source code from the latestPAMLrelease. If you want to installPAMLfrom source code, please follow the details given above.
To download the executable files for an earlier version of PAML, PAML v4.9j, please download the compressed file following this link. If you have the latest latest Linux distros or Windows 10 or later, please follow the instructions above for each corresponding operating system to install PAML v4.9j – please note that it may not work due to software incompatibilities.
WARNING
Please use the instructions below only if you are trying to install an older version of PAML on Windows 9x/NT/2000/XP/Vista 7. Please note that we always recommend to use the latest stable version ofPAML; these instructions are kept here for the record.
paml4.9j.tgz on your local disk. Make sure the extension of the file (tgz) did not change with the download.paml4.9j/bin/ (you may see \ instead of / to separate the directories, i.e., paml4.9j\bin\). You may want to create a folder for local programs and move the PAML executables there. Below, you can find some notes for doing that:
C:\Users\Ziheng (please, replace this path with your own path, which will contain your username and your folders names). On Vista or Windows 7, this tends to be the default user folder. On Windows XP, you may see something like C:\Documents and Settings\Ziheng (again, this is an example, you may see your username instead).bin inside your user folder. In this example, C:\Users\Ziheng\bin. If you are the superuser/administrator of your PC, you may prefer the folder C:\bin. Whatever you choose, remember that this will be the folder for holding executable programs.User variables, now double-click on the variable Path to edit, then on the variable value field, and then move the cursor to the beginning. Now, insert the name of our program folder (e.g., in our example, C:\Users\Ziheng\Bin or C:\Bin, but please modify according to the folder you have created). Note that you will see a semicolon, which is used to separate the folder names. Be careful not to introduce any errors and keep using the semicolon if you need to include more folders. To save the new settings, please click OK.PAML executables. Copy or move the pre-compiled executables (baseml.exe, codeml.exe, evolver.exe, chi2.exe, etc.) from the paml4.9j\bin\ folder to the local programs folder you will have created (e.g., C:\Users\Ziheng\Bin\ in this example). After this, you can execute any of these programs from a command prompt wherever you are. If you like, you can include the version number by renaming the executable files (e.g., baseml.exe and codeml.exe to baseml4.exe and codeml4.exe, respectively). In that way, you will then run the program from the command line by typing codeml4 instead of codeml, which is useful if you have several versions installed on your PCLast, you can run a PAML program. Avoid double-clicking the program names from Windows Explorer or will not see any error messages on the screen when the program crashes. Instead, please start a command prompt box where you want to start the PAML program you want to run. For example, Start > Programs > Accessories > Command Prompt, or Start > Run and then type cmd and OK. You can right-click on the title bar and choose Properties to change the size, font, or colour of the window. Now, cd to the folder which contains your input files to tun the PAML program you want and type the name of its executable file (e.g., codeml, mcmctree, etc.). Here, we show how you can cd to the PAML folder (suppose you have extracted the archive into C:\Programs\paml4.9j\) and run the codeml program using the default files.
C:
cd \Programs\paml4.9j\
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 that you will have already defined. Therefore, the OS will find and execute the file codeml.exe in the C:\Users\Ziheng\Bin folder, which is the path that we exported in the environment variable in the example above (you will have a different path according to your username and the folder you chose). If you want, you could also use the absolute path to run the PAML programs, although you will need to remember this path! You could type something like the following:
C:\Programs\paml4.9j\bin\codeml
Some codeml analyses use amino acid distance (e.g., grantham.dat file in the dat directory of the PAML software) or substitution rate matrices (e.g., wag.dat file in the dat directory of the PAML software). You will then need to copy the necessary file to your current folder or specify its correct path in the control file to run the program. If the path is not correct or not found, the program will ask you to input the full path to that file until found.
PAML-XA graphical user interface called PAML-X was written by Bo Xu of Institute of Zoology, Chinese Academy of Sciences in Beijing. This GUI was written in Qt and should run on Windows, Mac OS X, and Linux, although the versions for Mac OS X and Linux may not be well tested.
WARNING
Please note thatPAML-Xis no longer maintained, so please use it at your own risk!
If, despite the warning above, you still want to try PAML-X, please download and install PAML (see above) and also PAML-X (links below). When using pamlX1.3.1 (GUI), you will need to use PAML V4.9 or later. When you run PAML-X for the first time, you need to specify the PAML folder name.
While the Windows executable seems to work fine for Windows users, some Linux/UNIX users may experience issues when compiling the GUI due to incompatibilities with the Qt package. If you are one of these users, you may want to try the following:
In the latest Linux versions, you should be able to have different versions of Qt packages. PAML-X requires Qt4, and so please install this version either via Synaptic or by typing the following command:
sudo apt-get install qt4-default
After that, you may want to move to the PAML-X folder with the source code and type:
qmake pamlX.pro
make
If there are no issues, the software should start compiling and, at the end, you should see an executable file called pamlX appear.
MCMCtree to date genome-scale datasets: dos Reis and Yang (2019) Bayesian molecular clock dating using genome-scale datasets. In: Anisimova (ed.) Evolutionary Genomics. Methods in Molecular Biology, vol 1910. Humana, New York, NY.mcmc3r R package to prepare your datasets before running MCMCtree for the following purposes:
MCMCtree output to estimate the marginal likelihood and compute Bayes factors here. This tutorial also describes how to perform parametric bootstrap of posterior probabilities.MCMCtree tutorials can be found here. Please note that they were written with an old version of MCMCtree and hence some options might be out of date (e.g., finetune and rootAge no longer need to be included in the control file). Nevertheless, the tutorials can be consulted for theoretical and technical information about the following analyses:
MCMCtree using the exact likelihood calculation.MCMCtree using the approximate likelihood calculation with both nucleotide and protein data.infinitesites to estimate divergence times with infinitely many sites.positive-selection GitHub repository here.If you use PAML, please cite the following:
If you use MCMCtree, please cite the following papers if you have used/run…
MCMCtree:
mcmc3r R package if you use it (tutorial here).BASEML and MCMCtree can be found here.