This track displays the level of conservation of Zoo sequences at any given position. More precisely, it computes the p-value of observing a certain parsimony score for a given column of the multiple alignment, under the null model of neutral evolution.
Adam Siepel inferred the phylogenetic tree relating the Zoo species, as well as the length of each branch of the tree. This tree was used to measure the surprise of the conservation observed.
For each column of the multiple alignment produced by Webb Miller, the parsimony score for the columm was computed using Adam's phylogenetic tree. The p-value was then computed for that parsimony score under a null model of neutral evolution (see below for a description of the null model). Species with gaps in the column were ignored. A column received a low p-value if the parsimony score for the set of non-gap species was surprisingly low, given the divergence of these species. For column i, let Xi be the negative log of the p-value for that column.
For position i of the alignment, the score plotted on the track is the average of the Xj's in a window of 10 bp around position i.
This track was generated by Mathieu Blanchette, a former post-doctoral fellow with the UCSC Genome Bioinformatics Group. Many thanks to Adam Siepel for the phylogenetic inferrences and to Webb Miller for providing the multiple alignment of the Zoo sequences.