Getting started
Learning how to use a new command line program can be a real challenge!! I wrote this roadmap to try and give you a little guidance on how to get started using PASV. There are a lot of pages in the wiki, but if you follow along in this order, I think you will be able to get a good feel for the program!
Version 1 vs. Version 2
If you're looking for the source code or documentation for pasv
version 1 (e.g., to follow along with the PASV manuscript, see the GitHub archive and the old wiki.
Version 2 is easier to install and lets you use different methods for checking residues (multiple sequence alignment, hidden Markov models, and raw checking of alignment files).
Installation
The easiest way to start using PASV is probably by using one of the Docker images. It comes with everything you need to run PASV, including all external dependencies. If you are a Windows user, this is currently your only way to use PASV.
Installing PASV is also easy if you use one of the precompiled binaries. This is actually the easier option if you already have one of Clustal Omega, MAAFT, or HMMER installed.
Alternatively, if you are an OCaml programmer or want to run the test suite locally, you can install PASV from source.
PASV CLI
An overview of the PASV CLI is available as well as examples for using PASV.
PASV Details
Once you've gone through the above introductory material, you will probably want to check out a few more pages. Check out the following pages to learn about picking good references and key residues. We spent a lot of time working out best practices for these things in the manuscript, so I encourage you to check it out!
Finally, if you're stuck and need help, open an issue and I will try and clear up any difficulties you're having!