This track shows a measure of evolutionary conservation in twelve Drosophila species, mosquito, honeybee and red flour beetle, based on a phylogenetic hidden Markov model (phastCons). Multiz alignments of the following assemblies were used to generate this annotation:
Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting.
The phastCons parameters for the 15-way Drosophila annotations are: expected-length = 23.8; target-coverage = 0.393; rho is set to the default value = 0.3.
The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM.
PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.