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Selection analyses in HyPhy

Presentation notes (in the assets folder) and example files in the data folder for how to perform selection analyses in HyPhy

For additional analyses, you will need the hyphy-analyses repository. Via git clone https://github.com/veg/hyphy-analyses.git

View the presentation (2023) at https://veg.github.io/selection-tutorial

Installation

Via Anaconda conda install -c bioconda hyphy

To compile from source follow the instructions at http://hyphy.org/download

Example commands

FitMG94

hyphy hyphy-analyses/FitMG94/FitMG94.bf --alignment data/WestNileVirus_NS3.fna --output results/WestNileVirus_NS3.fna.FITTER.json --lrt Yes

BUSTED

hyphy busted --srv No --alignment data/HIV-sets.nex --starting-points 5 --output results/HIV-sets.nex.BUSTED.json

hyphy busted --srv No --alignment data/WestNileVirus_NS3.fna --starting-points 5 --output results/WestNileVirus_NS3.fna.BUSTED.json

hyphy busted --srv No --alignment data/spike.fas --tree data/spike.tree --starting-points 5 --output results/spike.fas.BUSTED.json

aBSREL

hyphy absrel --alignment data/HIV-sets.nex --output results/HIV-sets.nex.aBSREL.json

hyphy absrel --alignment data/WestNileVirus_NS3.fna --output results/WestNileVirus_NS3.fna.aBSREL.json

hyphy absrel --alignment data/spike.fas --tree data/spike.tree --branches Internal --output results/spike.fas.aBSREL.json

MEME

hyphy meme --alignment data/HIV-sets.nex --output results/HIV-sets.nex.MEME.json

hyphy meme --alignment data/spike.fas --tree data/spike.tree --output results/spike.fas.MEME.json

hyphy meme --alignment data/spike.fas --tree data/spike.tree --output results/spike.fas.MEME-Internal.json --branches Internal

FEL

hyphy fel --alignment data/spike.fas --tree data/spike.tree --branches Internal --output results/spike.fas.FEL-Internal.json

hyphy fel --alignment data/spike.fas --tree data/spike.tree --branches Internal --output results/spike.fas.FEL-Internal-PBS.json --resample 100

hyphy fel --alignment data/WestNileVirus_NS3.fna --ci Yes --output results/WestNileVirus_NS3.fna.FEL-ci.json

SLAC

hyphy slac --alignment data/spike.fas --tree data/spike.tree --branches Internal --output results/spike.fas.SLAC.json

RELAX

hyphy relax --alignment data/AlphaDeltaSpike.fas --tree data/AlphaDeltaSpike.tree --test Delta --reference Alpha --starting-points 5 --output results/AlphaDeltaSpike.fas.RELAX.json

Contrast-FEL

hyphy contrast-fel --alignment data/AlphaDeltaSpike.fas --tree data/AlphaDeltaSpike.tree --branch-set Alpha --branch-set Delta --output results/AlphaDeltaSpike.fas.CFEL.json

GARD, FMM, BSMH