New functionality for the June 3rd, 2008 update.

[1] Protein/nucleotide data
Datamonkey now accepts protein and nucleotide data for upload and permits some analyses to be run on them. Check Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for the current list.


[2] Model selection for protein data
Datamonkey includes a number of empirical models (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) that can be fitted to a protein alignment and the best model selected based on AIC, c-AIC or BIC (much like David Posada's ProtTest)

[3] Ancestral sampling for BGM/Spidermonkey
Bayesian Graphical Models can now be fitted using not just the most likely ancestral reconstruction but also a number (currently 100) of ancestral reconstructions sampled in proportion to their likelihood. BGM results (tables, plots) etc will also include additional information about how many ancestral replicates support a particular edge.

[4] Protein/nucleotide data for BGM/Spidermonkey
Bayesian Graphical Models can be run on substitutions mapped to tree branches for protein and nucleotide data.

[5] Side-by-side mutation map comparisons for BGM/Spidermonkey
The level of concordance/discordance of mapped substitutions for inferred pairs of interacting sites can be visualized on the tree and shown in a table for easier comparison.

SLKP