VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

Thanks for taking an interest in our pipeline. We hope you find the resources we provide here useful in getting you set up to analyse and interpret your data.

To reference VESPA: https://peerj.com/preprints/1895/

Documentation is now hosted on ReadTheDocs

Installation

The main VESPA wrapper is written in Python, while the CodeML wrapper is written in Perl.

To begin, we recommend downloading a versioned tarball from the releases page.

Once downloaded, install as follows:

$ tar -xvzf VESPA.tar.gz
$ cd VESPA
$ chmod +x vespa.py
$ sudo mv vespa.py /usr/local/bin

Easier installation with Anaconda (new)

This approach installs many but not all of the binary dependencies

Install Anaconda or Miniconda
Download release, decompress and cd inside it
Create the conda environment: conda env create -f vespa_conda.yml
Activate it: source activate vespa27
Run VESPA with python vespa.py

Dependencies

Perl dependencies

VESPA requires several Perl scripts and modules to be fully operational. The Perl dependencies may be found alongside vespa.py within the tarball.

The following will install these modules on most systems.

$ tar -xvzf VESPA.tar.gz
$ cd VESPA
$ chmod +x \*Codeml\*.pl
$ sudo mv \*Codeml\*.pl /usr/local/bin
$ sudo mv CodemlWrapper/ /Library/Perl/5.XX/
Note: Replace “5.XX” in the following command to the version of perl used by your system. (perl –v)

DendroPy

VESPA requires users to install the DendroPy Python library (version 4.0). Instructions for installing DendroPy

Using VESPA

We have written a manual that will take you through the process step by step. This is constantly evolving with feedback with feedback from our users, and the latest version is hosted as vespa-evol on ReadTheDocs.

Issues

If you encounter an issue with VESPA, please open a GitHub issue and we'll do our best to help.