Question: Phylop Results Interpretation
gravatar for Fedor Gusev
6.9 years ago by
Fedor Gusev210
Russian Federation
Fedor Gusev210 wrote:

I've downloaded a multiple sequence alignment of 100 species for a fragment of human ACTB gene (specifically for one of it's exons; coordinates are chr7:5567961-5568345) from UCSC table browser. The file itself is available at When looking at this region in UCSC genome browser, it seems to be conservative: enter image description here However, when I run PhyloP on this alignment, p-value of conservation is 1:

$ wget -q -O ACTB.some_exon.maf ''
$ wget -q ''
$ phyloP hg19.100way.phyloP100way.mod ACTB.some_exon.maf
WARNING: pruned away leaves with no match in alignment (papHam1, pteVam1, echTel2, dasNov3).

P-values for number of substitutions observed in 'ACTB.some_exon.maf' given 'hg19.100way.phyloP100way.mod'

p-value of conservation: 1.000000e+00
p-value of acceleration: 0.000000e+00

null distrib: mean = 883.012452, var = 910.568347, 95% c.i. = [824, 943]
posterior distrib: mean = 4554.053300, var = 4839.759760

Am I running PhyloP incorrectly?

ADD COMMENTlink modified 6.8 years ago by Biostar ♦♦ 20 • written 6.9 years ago by Fedor Gusev210
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2262 users visited in the last hour