AOC PS & snakemake pipeline, very similar to PanAdapt

[hoelzer]

Step 1. Codon-aware alignment from protein and gene transcript files
Step 2. Recombination detection (via GARD)
Step 3. Tree inference (ML Tree inference, preferably IQ-TREE or RAxML).
Step 4. Selection analyses: this includes (MEME, FEL, FUBAR, BUSTED Model testing, MEME, aBSREL, SLAC, BGM, FMM, etc)
Step 4. Lineage assignment and tree annotation (Custom script)
Step 5. Selection analyses on lineages (RELAX, CFEL)

https://github.com/aglucaci/AnalysisOfOrthologousCollections

paper: https://arxiv.org/abs/2406.09522
by Alexander Lucaci, Sergei Pond

Alexander is giving a workshop on PS analysis next week here in Romania, so I will also meet him.

@StefanFrankBio I think this might be really interesting to look into and merge code w/ your pipeline, potentially also re-initiating the contact to Sergei Pond.