This is an implementation of the PASTA (Practical Alignment using SATe and TrAnsitivity) algorithm. This version is currently for testing purposes only.
The current version of this code is heavily based on the SATe code (http://phylo.bio.ku.edu/software/sate/sate.html) Future versions would start from a fresh implementation.
Current version of PASTA has been developed and tested entirely on Linux. It probably works on MAC machines as well. Windows won't work currently, but is planned for future versions.
You need to have:
- Python
- Dendropy (http://packages.python.org/DendroPy/)
- Java (for OPAL)
Download the zip file, extract it and cd into the pasta.1.1.0/pasta. Then run:
python steup.py develop
You probably need to add a sudo in front of that command. If you don't have root access, use --prefix to install in a different location.
That different location needs to be part of your PYTHONPATH environmental variable. Email: smirarab@gmail.com for installation issues.
Download the zip file, extract it and cd into the pasta.1.1.0/pasta.
If you are installing on MAC, you need to go through some additional steps. After you extract the zip file, go to pasta.1.1.0, and clone the following git repository:
https://github.com/sate-dev/sate-tools-mac
You can use git clone command to clone the repository, or just download the zip file (https://github.com/sate-dev/sate-tools-mac/archive/master.zip).
Then run the setup.py command as described under Linux.
To run, use:
python run_pasta.py -i input_fasta -t starting_tree