[Inparanoid] Ortholog detection and false positives

[Praveen Raj]

Hello,

I'm comparing the proteomes of two fungal strains (recently drafted and
annotated by  genome assembly) to identify orthologs. I could successfully
ran the program passing the two protein fasta files and identified ~101
ortholog groups.

However I suspect that there could be false positives in the results as
these proteomes were annotated by BLAST methods against NCBI and Uniport by
the publisher. Is there any mechanism to filter out such false positive
orthologs based on Inparanoid database sequences (another round of
comparison)?

Please advise how do we achieve this.

Thanks
Raj
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