Notes on creation of the tracks in http://data.broadinstitute.org/compbio1/PhyloCSFtracks/galGal4/20160701:

PhyloCSF was run with the "fixed" strategy using the 49birds parameters on every codon in every frame on each strand in the galGal4 chicken assembly. The frame of a codon is defined as the remainder mod 3 of the lowest nominal base of the codon, counting the first base of a chromosome as 1. 

Alignments were extracted using a pre-publication version of the 49 sauropsids alignment.

The scores were smoothed using a hidden markov model (HMM) with 4 states, one representing coding regions and three representing non-coding regions. The emission of each codon is its PhyloCSF score. The ratio of the emissions probabilities for the coding and non-coding models are computed from the PhyloCSF score, since it represents the log-likelihood ratio of the alignment under the coding and non-coding models. The three non-coding states have the same emissions probabilities but different transition probabilities (they can only transition to coding) to better capture the multimodal distribution of gaps between same-frame coding exons. These transition probabilities represent the best approximation of this gap distribution as a mixture model of three exponential distributions, computed using Expectation Maximization.

The HMM defines a probability that each codon is coding, based on the PhyloCSF scores of that codon and nearby codons on the same strand in the same frame, without taking into account start codons, stop codons, or potential splice sites.

PhyloCSF+0.bw shows the log-odds that codons in frame 0 on the '+' strand are in the coding state according to the HMM, and similarly for strand '-' and frames 1 and 2.

PhyloCSF+0Regions.bb, etc., show the regions that are coding in the most-likely-path through the HMM. They are something like predicted exons, except that they don't look at splice sites, start codons, or stop codons so the boundaries are approximate. The gray scale is an indication of the maximum log-odds that any codon in the region is coding according to the HMM.

PhyloCSFpower.bw shows the branch length score at each codon, .i.e., the ratio of the branch length of the species present in the local alignment to the total branch length of the 29-mammals tree. It is an indication of the statistical power available to PhyloCSF. Codons with branch length score less than 0.1 have been excluded altogether (from all tracks) because PhyloCSF does not have sufficient power to get a meaningful score at these codons. Codons with branch length score greater than 0.1 but much less than 1 should be considered less certain.