PhyloP basewise conservation


PhyloP basewise conservation score derived from Multiz alignment of 46 vertebrate species. This series includes two SGA files, one for all vertebrates and one for placental mammals only.


Files downloaded from UCSC genome browser database:


From H. sapiens (Feb 2009 GRCh37/hg19).
Filename Description Feature GEO-ID
1 phylop_vert.sga PhyloP vertebrate 46way (score >= 2) PhyloP -
2 phylop_placental.sga PhyloP placental mammal 46way (score >= 2) PhyloP -

Technical Notes

The sources files are in WIG fixedStep format. Conversion into SGA was carried out with an ad hoc Perl script. In order to keep the SGA files reasonably compact, only positions with phyloP scores ≥2 were considered. The original phyloP score is reflected in the count (5th) field of the SGA files. The real phyloP score values were first dimished by one and then rounded down to the nearest integer:

   counts = int(phyoP_score-1)
UCSC also provides phyloP files for Primates. Those were not converted into SGA files, as they primarily contain negative values reflecting accelerated evolution rather than conservation.


  1. Pollard KS, Hubisz MJ, Siepel A.
    Detection of non-neutral substitution rates on mammalian phylogenies Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363