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rhysnewell / Lorikeet

Strain resolver for metagenomics
GNU Affero General Public License v3.0
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evolve not available #59

Open jianshu93 opened 2 months ago

jianshu93 commented 2 months ago

Hi @rhysnewell,

I remember that I used the evolve subcommand 2 years ago when this was still under development . As also shown in readme, but the actual evolve subcommand is not available any more when installing the newest version 0.8.2. How do I use it when I have a genome and reads and I want know dD/dS for each gene under a give read alignment filtering threshold?

Thanks,

Jianshu

rhysnewell commented 2 months ago

Hi @jianshu93,

Apologies but that subcommand was just merged into the standard call command. If you want to have the same output as evolve, just add the calculate-dnds parameter. I also recommend adding the calculate-fst command

The docs will be updated with the intended usage

Cheers, Rhys