Datamonkey.org help

Analyze your data

Available topics.

Tutorial.

An example based tutorial on using Datamonkey. An excellent 'Getting Started' resource!

Data files.

Preparing data files for Datamonkey.org: general guidelines and common mistakes to avoid.

Site-by-site selection.

There are three available methods to test selection at a single codon site:

SLAC (up to 150 sequences): The fastest and most conservative method. Use it for large datasets (50 sequences or more) and to obtain substitution maps at each site - a useful feature for visualizing the evolutionary process.
FEL/IFEL (up to 100 sequences): The best overall method, in terms of tradeoff between statistical performance and computational expense. Use it for intermediate to large datasets (50 sequences or more) and if you wish to obtain good site-by-site substitution rate estimates. Use IFEL to test for sitewise selection on internal branches of the tree.
REL (up to 40 sequences): REL is an extension of familiar codon-based selection analyses pioneered by Nielsen and Yang and implemented in PAML. Importantly, REL allows synonymoys rate variation. It is often the only method that can infer selection from small (5-15 sequence) or low divergence alignments, but also the method that makes the most assumptions and susceptible to high rates of false positives in extreme cases.

Overall signature of selection. PARRIS (up to 40 sequences)

An extension of standard likelihood ratio tests to deal with recombinant data. Useful for answering the question: is there evidence of positive selection anywhere in my alignment?

Lineage specific selection. GA Branch (up to 25 sequences)

A genetic algorithm based data mining procedure which automatically partitions all branches in the tree into several selective regimes (and infers the most appropriate regimes), and performs multi-model inference for increased robustness.

Evolutionary interations between sites. Spidermonkey (up to 150 sequences)

Use a Bayesian Graphical Model (BGM) applied to reconstructed evolutionary histories of individual sites to find evidence of co-evolution between sites in an alignment.

Other topics.

Post your questions on our user assistance message boards if none of the above topics match your query.

Sergei L. Kosakovsky Pond, Art Poon and Simon D.W. Frost, 2004-2008