I have a need to search for single-copy conservative orthologs within several plant genomes and used BUSCO tool for that. However, I found that the results produced by different versions on the same genome assemblies are very different (ca. 20% difference between v.3.0.2 and v.4.1.4. by quantity, but ca. 50% by BLAST). Even more, different runs of the same version (in particular, v.4.1.4) on the same genome assemblies and with the same parameters and lineage dataset also producing slightly different results (the quantitative difference is ca. 30-40 COS from ca. 2000).
Therefore I am interested to check the results independently and would be very grateful if anybody could suggest an alternative software suitable for this task.
Thank you in advance,
Best regards,
Andrii Tarieiev
OrthoMCL (https://pubmed.ncbi.nlm.nih.gov/12952885/) is probably one of the most widely used algorithms to identify orthologs within eukaryotic genomes.
Dear Francisco Callejas-Hernández, thank you very much for the suggestion. The problem is that OrthoMCL works with protein sequences and proteomes, but I do need to work with genomic data directly without converting it to amino acid codes.
Use OrthoFinder (https://github.com/davidemms/OrthoFinder)
It generates a folder with all single-copy orthologs in fasta format. It uses the same approach as OrthoMCL, but WAY easier to run. After version 2.4.1, you can use DNA sequences also, gene models in this case, not assemblies.
If you only have the genome assemblies, I strongly suggest annotating them using tools like MakerP (http://www.yandell-lab.org/software/maker-p.html). You will not get farther without it.
MakerP would be a good choice for the assembled genome data.
I do agree with Andrei Stecca Steindorff
I agree with Andrei Stecca Steindorff on latest version of OrthoFinder.
I think you'd better annotate the genome first, next you can use tools to do the gene clustering part. In addition to Maker-p, GeneWise and GeMoMa are also good chocie for fast gene annotation. Orthofinder and OrthoMCL are most popular tools in gene clustering, I also agree with Andrei Stecca Steindorff , Orthofinder is better. And if you are dealing with animal genomes, TreeFam(http://www.treefam.org/) database can be refered
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