14-6-20.2

This release is an update of the tree released on 14-6-20.

The code to produce the alignments and trees in this release is identical to that release, except for one detail. In this updated release the maximum likelihood tree has been improved by re-running it with the following commandline:

fasttree -nosupport -nt -gamma global.fa

This differs from the previous release only in that it does not use fasttree's -fastest tag.

I did this because manual examination of the tree from 14-6-20 showed a large and probably misplaced clade. Re-running the tree with the commandline above leads to a large improvement in the log likelihood from -382048.463 in the original release to -381841.805 in this updated release. In addition, the probably-misplaced clade has moved back to what is likely to be the correct position at the root of the tree. Regardless, this tree has a better likelihood so should be preferred.

I exploring improvements to the tree estimation. Releases after 17-6-20 (which was started before this solution was figured out) will include these improvements, and I'll only release the tree from 17-6-20 if the clade misplaced on 14-6-20 is in the correct position.

The bootstrap values on the two trees below were mapped using exactly the same set of bootstrap trees produced in the original 14-6-20 release. And, just as for the 14-6-20 release, the trees were then run through TreeShrink to remove taxa on long branches.