VESPA

“VESPA: Very large-scale Evolutionary and Selective Pressure Analyses”

Thanks for taking an interest in our pipeline. Everything you need to use this software is on this page. 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/?td=wk

To download VESPA from GitHub:

https://github.com/aewebb80/VESPA

The VESPA software is released under the GNU general public license as per: http://www.gnu.org/licenses/gpl-3.0.en.html

 

Installing VESPA:

VESPA1.0b is written in python and therefore should be compatible with most systems.

The VESPA software is available to download on GitHub from the following link:

https://github.com/aewebb80/VESPA

Once downloaded, it can be installed as follows:

$ tar -xvzf VESPA-1.0b.tar.gz

$ cd VESPA-1.0b

$ chmod +x vespa.py

$ sudo mv vespa.py /usr/local/bin

 

Dependencies:

Perl dependencies: VESPA requires users to install multiple perl scripts and modules to be fully operational. The perl dependencies may be found alongside vespa.py within the program tarball. Once downloaded, it can be installed as follows:

$ tar -xvzf VESPA-1.0b.tar.gz

$ cd VESPA-1.0b

$ chmod +x *Codeml*.pl

$ sudo mv *Codeml*.pl /usr/local/bin

[Note: Replace “5.XX” in the following command to the version of perl used by your system. (perl –v)$ sudo mv CodemlWrapper/ /Library/Perl/5.XX/]

DendroPy: VESPA requires users to install the DendroPy python library (version 4.0). Instructions to installing DendroPy can be found at the following link: https://pythonhosted.org/DendroPy/#installing

 

Using VESPA:

We have written a manual that will take you through the process step by step. Please download the manual from here “Your_VESPA_Manual“. And follow the steps. If you have any difficulty please let us know. To get started we highly recommend you take our tutorial located here “VESPA_Tutorials.tar.gz“, which is specially designed for the new user.

 

VESPA Phases, File Formats and External Software Compatibilities:

Phase

Purpose Supported Input Type Supported File Formats
1 Data Preparation Sequences1 FASTA
2 Homology Searching BLAST/HMMER output BLAST tabular, HMMER standard
3 Alignment Assessment and Phylogeny Reconstruction Alignments1 FASTA, NEXUS, PHYLIP
4 Selective Pressure Analysis Preparation Phylogenies with alignments1 Trees: Newick, NEXUS; Alignments: See above
5 Selective Pressure Analysis Assessment codeML output VESPA formatted codeML output

1Indicates phases of VESPA that incorporate third-party programs.

A little extra help:

If you would like a little extra help we have generated the following videos that take you through some of the more involved stages of the pipeline. The videos are listed below (note our name for VESPA was Lamp when we made these videos):

(1) Phase 1 tutorial video: phase1

(2) Phase 2 tutorial video: phase2

(3) Phase 3 tutorial video: phase 3

(4) Phase 4 tutorial video: phase4

(5) Phase 5 tutorial video: phase5

 

Feedback:

If you have any feedback on usability please do not hesitate to contact us: drmary.oconnell@gmail.com and tug41380@temple.edu