Anolis Trial
From BEAST Software
WARNING: This page contains work in progress -- any results on this page are subject to change and have not undergone any peer-review. Use this information at your own risk.
The Anolis data is an alignment of a partial protein-coding gene sequence from 29 Anolis lizards (first 1038bp of NADH2 gene). This dataset has a single representative of 29 different recognised species of Anolis lizards, so that the tree should be thought of as a phylogenetic gene tree, rather than a coalescent genealogy. Nevertheless it gives a good case of highly variable sequence data.
Initially I chose to do a comparison that made for the simplest MrBayes input file. So the substitution model chosen was F81 (equilibrium base frequencies). By default the simplest model in BEAST is HKY + empirical base frequencies but with a couple of small changes to the BEAST input XML I was able to support F81 with estimated base frequencies:
BEAST 1.4.3 input file: anolis29.xml
MRBAYES 3.1.2 input file: Anolis29.nex
Here I am just recording some initial forays to help us formulate a more systematic plan.
| Program | Time | Chainlength | 50% credible set | 95% credible set | ESS LnL | ESS TL | ~ESS LnL / Hour | ~ESS TL / Hour | Tester | Notes |
|---|---|---|---|---|---|---|---|---|---|---|
| Anolis Trial BEAST 1.4.3 | 60 minutes | 10,000,000 | 22 | 370 | 7444 | 1509 | 7444 | 1509 | AJD | Macbook Pro Intel Core Duo 2GHz |
| Anolis Trial BEAST 1.5a MCMCMC | 0.5 hours | 2,000,000 | 26 | 587 | 3527 | 1622 | 7054 | 3244 | AJD | Macbook Pro Intel Core Duo 2GHz |
| Anolis Trial MRBAYES 3.1.2 | 5.01 CPU hours | 2 * 10,000,000 | 16 / 15 | 261 / 232 | 6796 + 7298 | 16010 + 16640 | 2813 | 6517 | AJD | Macbook Pro Intel Core Duo 2GHz |
| Anolis Trial MRBAYES 3.1.2 MCMCMC | 4.5 hours | 2 * 2,000,000 | 20 / 19 | 369 / 346 | 4809 + 4580 | 16780 + 17780 | 2086 | 7680 | AJD | Macbook Pro Intel Core Duo 2GHz |
