Reconstruction of orthology/paralogy relationships

It looks like material for at least two lab meetings is developing here... e.g. one on basic algorithms (reconciliation of gene/species trees, MCMC approaches...) and another on how these algorithms are being used to develop ortholog databases. Although, perhaps we can consider if this is not the optimal split, since Jason would like to compare OrthoMCL to InParanoid. Evolution of gene families may be a third area, though this breaks somewhat from the idea of considering essentially algorithmic approaches in these meetings - IH

I am also fine just going briefly over pros/cons of the practical aspects of these different tools if no-one else cares that much about OrthoMCL vs InParanoid. I think we ought to spend at least one meeting on theory of gene/species tree and how this can be applied to orthology detection cleanup after homologs have been identified. The evolution of families may be separate as you say - we can at least talk about algorithmic aspects of a Birth-Death model - JS

Automated database construction

See AutomatedOrthologDatabaseLabMeeting.

Evolution of paralogous families

See GeneFamilyEvolutionLabMeeting.

Gene tree/species tree reconcilation

See GeneSpeciesTreeReconciliationLabMeeting.