These tracks show conservation scores and single-base-pair resolution significantly conserved or accelerated elements among two different alignments. The alignments used are:
We generated site-by-site conservation scores using phyloP(Pollard et al. 2010) with the --method LRT and --mode CONACC options. These scores were then corrected for multiple-testing using the BH FDR-controlling method(Benjamini and Hochberg 1995). Any site with a resulting q-value of less than 0.05 (for a <5% expected FDR) was deemed significantly conserved or accelerated.
For the 100-way, we used the scores already generated by the UCSC browser as part of their human conservation tracks. ### Neutral model PhyloP requires a neutral model to generate its scores. Our 200M neutral model was generated based on neutrally-evolving ancestral repeats using phyloFit (from the PHAST(Hubisz, Pollard, and Siepel 2011) package) and the REV model, fit using the EM strategy.
| Alignment | Neutral model |
|---|---|
| 242-way 200M | Model file |
| 100-way | Model file |
The 200 Mammals consortium, as well as the UCSC Genome Browser, provided the input data.
Please contact Joel Armstrong or Benedict Paten with questions.
Benjamini, Yoav, and Yosef Hochberg. 1995. “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society. Series B (Methodological) 57 (1): 289–300. http://www.jstor.org/stable/2346101.
Blanchette, Mathieu, W. James Kent, Cathy Riemer, Laura Elnitski, Arian F A Smith, Krishna M. Roskin, Robert Baertsch, et al. 2004. “Aligning multiple genomic sequences with the threaded blockset aligner.” Genome Research 14 (4): 708–15. https://doi.org/10.1101/gr.1933104.
Hubisz, Melissa J., Katherine S. Pollard, and Adam Siepel. 2011. “PHAST and RPHAST: Phylogenetic analysis with space/time models.” Briefings in Bioinformatics 12 (1): 41–51. https://doi.org/10.1093/bib/bbq072.
Pollard, K. S., M. J. Hubisz, K. R. Rosenbloom, and A. Siepel. 2010. “Detection of nonneutral substitution rates on mammalian phylogenies.” Genome Res. 20 (1): 110–21.