Description
This track shows the multiple genome alignment of ten Drosophila genomes. It also shows the measurements of evolutionary conservation using phastCons and phyloP from the Phylogenetic Analysis with Space/Time models (PHAST) package.
Methods
Whole Genome Alignments
The whole genome alignments were produced using LAST, and then processed by the last-split and last-postmask programs to identify orthologous regions between the nine Drosophila genomes and the D. willistoni genome assembly. The split-alignments between nine Drosophila genome assemblies and Drosophila willistoni were combined into a multiple sequence alignment using ROAST. The ROAST alignments were processed using the utilities developed by the UCSC Genome Bioinformatics Group for display on the UCSC Genome Browser.
The following table shows the ten Drosophila genome assemblies used to construct the ROAST Alignments track:
Phylogenetic Tree Model
The non-conserved model used by phastCons and phyloP was constructed by the phyloFit program from the PHAST package using the general reversible (REV) substitution model.
PhastCons Conservation
Conserved elements were identified by phastCons using an expected length of 45 and a target coverage of 0.3. The conserved model is defined as a scaled version of the non-conserved model with the scaling factor rho of 0.4.
PhyloP Conservation
The conservation score for each site of the alignment was determined by phyloP using the likelihood ratio test (LRT) and the CONACC mode. Sites with positive scores indicate conservation while sites with negative scores indicate acceleration.
References
Finet C, et al. DrosoPhyla: Resources for drosophilid phylogeny and systematics. Genome Biol Evol. 2021 Aug 3;13(8):evab179.
Frith MC, Kawaguchi R. Split-alignment of genomes finds orthologies more accurately. Genome Biol. 2015 May 21;16(1):106. doi: 10.1186/s13059-015-0670-9.
Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan;12(1):41-51.
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
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