Tools for de novo orthology prediction among genomes. What to choose?

More Panagiotis Provataris's questions See All

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Can you fill a quick questionnaire?

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How can I remove false positives using the calculated bisulfite conversion rate in a WGBS experiment?

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Hello I would like to ask you how we can add the different sulfur compounds in hysys for the crude distillation? Thank you!

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Study bringing together genomics, proteomics etc together

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Felipe Aguilera

Hi Panagiotis,

Orthofinder does exactly what you need. https://github.com/davidemms/OrthoFinder

Although it uses many additional software, it is super easier to use and gives you a list of orthologs genes in a 1:1 way. If you are planning to find orthologs genes among 50 species, I recommend you to use diamond for blast step instead of traditional blastp.

Panagiotis Provataris

Thank you Felipe, I will check this :)

John Vollmers

Ican also recommend:

- proteinortho (Bidirectional Best Blast-hit based) : https://www.bioinf.uni-leipzig.de/Software/proteinortho/

-get_homologues (BDBH, COG-trianlges and/or OrthoMCL-based): https://github.com/eead-csic-compbio/get_homologues