-
Notifications
You must be signed in to change notification settings - Fork 24
Omega Test
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.
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.