This track shows measurements of evolutionary conservation using the phyloP program from the PHAST package, for all genomes in the comparative assembly hub. The multiple alignments were generated using progressiveCactus.
PhyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. PhyloP is appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites). PhyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. PhyloP treat alignment gaps and unaligned nucleotides as missing data.
In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.
The conservation tracks of this comparative assembly hub were created using the phyloP package, which is part of HAL tools. The HAL's phyloP is a python wrapper for running the PHAST package phyloP program and building conservation tracks for all genomes in the HAL multiple alignment. The process starts with creating a neutral model using a reference genome and neutral regions provided. By default, it expects the neutral regions to be coding genes and uses 4fold degenerate site within those genes (which it extracts automatically). The neutral regions could also be ancestral repeats (or anything else). After the model is created, the program proceeds to compute the conservation scores for positions along the root genome. These scores are subsequently lifted over to the children genomes using the multiple alignment. Lastly, HAL phyloP computes the conservation scores for regions in the children genomes that do not align to the root genome. (Of note, the program uses the phylogenetic tree extracted from the HAL file if the tree is not specified.)
We thank Melissa Jane Hubisz and Adam Siepel for the PHAST package and their help with HAL phyloP.
The HAL phyloP package: Glenn Hickey, Joel Armstrong, Ngan Nguyen, Benedict Paten.
Siepel, A., Pollard, K. and Haussler, D.. New methods for detecting lineage-specific selection. Research in Computational Molecular Biology. 2006:190-205.
Hickey et al.. HAL: a hierarchical format for storing and analyzing multiple genome alignments.. Bioinformatics. 2013 May;29(10):1341-1342.