The programs from the PAML package by Ziheng Yang (1997, 2004) use a common input file format, containing parameters:

It's basically a list of key = value, and comments starts with an asterisk *:

Here is an short exerpt suited for the codeml program:

seqfile = myalignment.phy
treefile = mytree.nwk
model = 0  * possible values: 0: one omega for the tree; 1: one omega per branch (free-ratio model)

Parameter names described in PAML's manual are highlighted, and comments recognized as such.

The autodetection of the filetype works for all files with .ctl extension. I don't use this extension for another purpose but if you do, modify accordingly the ftdetect/PAML.vim commands.

I personally use Tim Pope's Pathogen as my plugin manager (and recommend it).

With Pathogen, simply clone this repository inside ~/.vim/bundle/.

Likely buggy, but it fits my needs so far.