identity threshold of DIAMOND

[scientisth]

What is the default identity threshold of DIAMOND in Orthofinder? How to modify it?

[Jonathan-Holmes-Bioinformatics]

Hi scientisth,

The default E-value is 0.001.

diamond blastp -d DATABASE -q INPUT -o OUTPUT --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1

All defaults can be viewed and modified by editing the config.jon located in OrthoFinder/scripts_of/config.json