PhastCons Vert30, Genome Conservation Scores


This track shows multiple alignments of 30 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and two subsets (euarchontoglire and placental mammal). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

The species are divided into three different groups. The euarchontoglires subset (10 species plus mouse), the placental mammal subset (19 species plus mouse), and all 30 vertebrate species together. These three measurements produce the same results in regions where only euarchontoglires appear in the alignment. For other regions, the non-euarchontoglires species can either boost the scores (if conserved) or decrease them (if non-conserved). The placental mammal conservation helps to identify sequences that are under different evolutionary pressures in mammals and non-mammal vertebrates.

PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns.

The phastCons scores represent probabilities of negative selection and range between 0 and 1.

PhastCons treats alignment gaps and unaligned nucleotides as missing data, and it was run with the same parameters for each species set (vertebrates, placental mammals, and euarchontoglires). Thus, in regions in which only euarchontoglires appear in the alignment, all three sets of scores will be the same, but in regions in which additional species are available, the mammalian and/or vertebrate scores may differ from the euarchontoglire scores. The alternative plots help to identify sequences that are under different evolutionary pressures in, say, euarchontoglires and non-euarchontoglires, or mammals and non-mammals.

The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from Adam Siepel at Cornell University.

Details of the alignment parameters are noted in the genomewiki Mm9 multiple alignment page.

The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 17-vertebrate alignment, this track includes 13 new species and 4 species with updated sequence assemblies. The new species consist of seven high-coverage (5-8.5X) assemblies (orangutan, marmoset, horse, platypus, lizard, and two teleost fish: stickleback and medaka) and six low-coverage (2X) genome assemblies from mammalian species selected for sampling by NHGRI (bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat). The cow, chicken, fugu, and zebrafish assemblies in this track have been updated from those used in the previous 17-species alignment.


PhastCons scores were downloaded from the UCSC Genome Browser via URL:


From M. musculus (July 2007 NCBI37/mm9).

Filename Description Feature GEO-ID
1 phastcons.sga PHASTCONS VERT30 PHASTCONS -

Technical Notes

Pairwise alignments with the mouse genome were generated for each species using blastz from repeat-masked genomic sequence. Lineage-specific repeats were removed prior to alignment, then reinserted. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net.

An additional filtering step was introduced in the generation of the 30-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best").

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

phastCons is a phylogeneitc method that relies on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 30-way alignment.

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. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.


  1. Siepel, A. and Haussler, D et al.
    Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005). PMID: 16024819