Could I calculate AAI of eukaryotes by CompareM?

Question

Could I calculate AAI of eukaryotes by CompareM?

DustinChen1986 opened this issue 4 years ago · comments

DustinChen1986 commented 4 years ago

Could I calculate AAI of eukaryotes by CompareM, or I can combine Orthofinder or OrthoMCL with CompareM to calculate AAI between eukaryotic genomes?

Donovan H. Parks · Answer 1 · Mon Jul 06 2020 21:49:32 GMT+0800 (China Standard Time)

CompareM is designed with bacterial and archaeal genomes in mind. In particular, it uses Prodigal to call genes which assumes the input genome in bacterial or archaeal. However, if you provide the called genes it should work for Euks.

DustinChen1986 · Answer 2 · Wed Jul 08 2020 22:58:18 GMT+0800 (China Standard Time)

Thank you for your reply.