Subworkflow to look for long-range HGT

[austinhpatton]

Description of feature

It would be great if we could create a subworkflow (likely best to be able to toggle this on/off as needed) that would, for each gene family, search for long-range HGT from other distantly related groups of organisms into the focal group for which the most extensive phylogenetic work is being conducted. For instance, this could be a way to identify which gene copies transferred from bacteria into some eukaryotic group.

For instance, this could involve using an AlienIndex type of approach to asses evidence, for each protein, for lateral transfer from some outside group by blast within gene families and to taxonomic dbs of distantly related groups to identify putative long-range HGT. We then could use phylogenetic placement of those distant hits into the gene-family trees inferred for the focal/in-group. Could be a way to reduce the scope of the challenge, while allowing us to detect and distinguish between short/long-range HGT events.