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PASTA

This is an implementation of the PASTA (Practical Alignment using SATe and TrAnsitivity) algorithm. This version is currently for testing purposes only.

All questions and inquires should be addressed to our user email group: pasta-users@googlegroups.com

Acknowledgment

The current version of this code is heavily based on the SATe code (http://phylo.bio.ku.edu/software/sate/sate.html). Refer to sate-doc directory for documentation of the SATe code.

INSTALLATION

From pre-build MAC image file

1- Download the MAC application .dmg file from the project website. 2- Open the .dmg file and copy its content to your preferred destination. 3- Simply run the PASTA app

From Source Code

Current version of PASTA has been developed and tested entirely on Linux. It has been tested on MAC as well, but less extensively. Windows won't work currently (future versions may or may not support Windows).

You need to have:

Insallation steps:

  1. Open a terminal and create a directory where you want to keep PASTA. e.g. mkdir ~/pasta-code. Go to this directory. e.g. cd ~/pasta-code.

  2. Clone the PASTA repository from our github repository. For example you can use git clone https://github.com/smirarab/pasta.git. If you don't have git, you can directly download a zip file from the repository and decompress it into your desired directory.

  3. Clone the relevant "tools" directory (these are also forked from the SATe project). Note that there are different repositories for linux and MAC. e.g., you can use git clone git@github.com:smirarab/sate-tools-linux.git on Linux or git@github.com:smirarab/sate-tools-mac.git on MAC. Or you can directly download these as zip files for Linux or MAC and decompress them in your target directory for PASTA code.

  4. cd pasta

  5. Then run:

python setup.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 pasta-users@googlegroups.com for installation issues.

EXECUTION

To run the command-line, use:

python run_pasta.py -i input_fasta -t starting_tree --auto

The --auto option picks the appropriate configurations automatically for you.

Run python run_pasta.py --help to see PASTA's various options.

To run the GUI version,

  • if you have used the MAC .dmg file, you can simply click on your application file to run PASTA.
  • if you have installed from the source code, cd into your installation directory and run
python run_pasta_gui.py

Starting Trees

Since version 1.4.0, PASTA uses the procedure described in the paper for estimating the starting alignment and trees if none is given.

The PASTA approach for getting the starting tree can be summarized as:

  1. Choose a random subset of your sequences (size 100).
  2. Get a MAFFT-linsi alignment on the subset.
  3. Build a HMMER model on the alignment of 100 subsets.
  4. Use hmmalign to align the remaining sequences into the small subset.
  5. Run FastTree on the output of step 4.

LICENSE

PASTA uses the same license as SATe (GNU Public License).