OMA standalone vs. OMAmer HOGs about omastandalone

[alpae]

Hi @biomendi

The big difference among OMAmer and OmaStandalone is that in the first case we map sequences to a (large) existing dataset of precomputed Hierarchical Orthologous Groups (HOGs) - usually all of OMA. The HOGs in there were initially also computed with the bottom up approach implemented in OmaStandalone.

If you compute HOGs with OmaStandalone, you don't use the knowledge that all the other genomes in OMA could bring. The HOGs are computed by recursively checking the completeness of pairwise ortholog relations among the sub-HOGs along the species tree. If you think your groups are too fragmented, this could have several reasons:

• the gene models in the species are fragmented -> this leads to splits as the LengthTol parameter breaks putative orthologs because they vary a lot in their length
• the sequences you are analyzing are relatively short -> the MinScore of 181 corresponds roughly to a bit score of 50 in a blast query, so it is quite stringent.
• you can also play around with the MinEdgeCompletenessFraction, to allow more aggressive merging of clusters (lower values)

Regarding the question of HOG-IDs: The StableIdsForGroups won't produce IDs similar to OMAmer. Those IDs are actually OMA browser release dependent (we try to provide a forward mapping of those IDs). The StableIdForGroups option rather produces an AA-fingerprint that is only found in this HOG. We haven't implemented this for the bottom_up version.

sorry for the late response. I hope it is still helpful.

Best wishes
Adrian