Ortholog Detection?

[Jome0169]

Hi there,

I've been scouring the documentation for how --onlyOrthologs works in hal2maf but haven't been able to figure it out. I'm working on identifying conserved sequences in a series of distantly related grass species, so accurate identification of orthologs is quite important. Can you either point me to a resource or give me a simple run down of how orthologs are identified from the alignments? Would it be best to supplement progressive cactus with a gene syntenty approach as well?

Thanks so much for any information you can provide.

[glennhickey]

Yeah, it's pretty poorly documented. cactus-hal2maf is a new wrapper for hal2maf that adds parallelization and a bunch of postprocessing. Its documentation is freshly updated here:

https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf

with the --onlyOrhtologs mode corresponding to the --dupdeMode ancestral option.