We have a set of about 5000 genes, each an alignment of about 90 species coding region.
For each gene, we need to
1) make a phylogenetic tree (using iQtree, which is quick)
2) estimate rates of molecular evolution (hyphy, which can take from 1 to 8 hours per gene)
We have been running this locally, have all the working scripts. We now need to scale out in a massively parallel framework for a quick turn around time. We expect with modest allocations, to be finished in < 1 week.