97805fb2ceb73357aa78aa94107148dc355d4e1c
mspeir
Tue Sep 22 08:36:22 2026 -0700
Conservation tracks: give the description pages a real Data Access section, refs #34803
The hgdownload link block on these pages had no header, and on 18 of them it sat
above the Description, which is where it got overlooked. Move it into an
diff --git src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
index 12d6dcb251b..22e74bf2692 100644
--- src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
+++ src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
@@ -37,30 +37,46 @@
http://compgen.cshl.edu/phast/). The program was given a
neutral model estimated from fourfold degenerate sites, as decribed for
the main conservation track. With these options, phyloP performs a
likelihood ratio test at each alignment column. This test compares a
null model in which the neutral branch lengths are all scaled by a
single scaling factor (a free parameter, estimated by maximum
likelihood), and an alternative model with separate scaling factors for
the clade of interest and the remainder of the phylogeny (both estimated
by maximum likelihood). To obtain an approximate p-value, the log
likelihood ratio of these two hypotheses is compared to an asymptotic
chi-squared null distribution, in the usual way. Scores are then
computed as -log 10 p-values. If the estimated rate for the clade of
interest is greater than the estimated rate outside that clade, the
score is negated, to indicate acceleration rather than conservation.
+
+Data Access
+
+The conservation scores can be retrieved for a single region or for a list of regions with the
+Table
+Browser, and joined with other annotations in the Data
+Integrator. For automated access, they are also served by our REST API.
+
+
+The files behind this track can be downloaded from our download server:
+
+
References
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS,
Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares
M, Vanderhaeghen P, and Haussler D.
An RNA gene expressed during
cortical development evolved rapidly in humans.
Nature. 443:167-172, 2006.
Siepel A, Pollard KS, Haussler D. New methods for detecting
lineage-specific selection.
Proc. 10th Int'l Conf.