Trimming columns with insufficient taxa is slow

[donovan-h-parks]

When inferring a tree, columns with insufficient representation across the taxa are trimmed. This step is currently very slow and can likely be improved. On the release 75 dereplicated bacterial tree is takes 25 minutes:

[2016-04-06 01:48:22] INFO: Trimming columns with insufficient taxa.
[2016-04-06 02:13:09] INFO: Trimmed alignment from 41155 to 41155 AA.