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mlin edited this page Sep 23, 2012 · 8 revisions

The "Omega Test" is a simplified operational mode of PhyloCSF that requires fewer pre-precomputed parameters about the phylogeny under analysis. In particular, while PhyloCSF requires both a phylogenetic tree and "empirical codon models" with thousands of parameters estimated from known coding and non-coding regions aligned in the species of interest, the "Omega Test" requires only a phylogenetic tree. On the other hand, the test is less accurate and slower than the standard PhyloCSF mode.

We have written a brief (dense) description of the mathematical details of the method.

Activating the Omega Test

To use the Omega Test with one of the existing phylogenies supported by PhyloCSF, simply add @--strategy omega@ to the command line. For example, the tal-AA alignment in the 12 fly genomes bundled with PhyloCSF:

$ ./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa
PhyloCSF_Examples/tal-AA.fa	score(decibans)	297.6235
$ ./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa --strategy omega
PhyloCSF_Examples/tal-AA.fa	score(decibans)	132.5892

The score is still reported as a likelihood ratio in units of decibans. In this example, the (known) coding region is given a highly positive score in both modes, but it is lower in magnitude with the Omega Test. This is typical: the Omega Test observes fewer informative features of the alignment than the full PhyloCSF method, and as a result usually reports less overall evidence one way or the other.

Providing a new phylogeny

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