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
<h2>Data Access</h2> in the usual place, after Methods and before Credits, and
add pointers to the Table Browser, the Data Integrator and the REST API, plus
the maf* and bigWig* command line tools.

134 pages: 55 had a download block that was moved and labeled, 56 get a list
built from hgdownload directories that were checked to exist, 21 have no
download directory of their own and so get the Table Browser and API pointers
only, and 2 already had a Data Access section that was reworked. Existing
download lists are unchanged apart from http -> https and an added
target="_blank".

Wording follows what each track actually holds, so the alignment-only pages do
not claim conservation scores and the Data Integrator is only mentioned where it
can really be used, since it does not handle MAF.

Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which
redirects; it is now multiz44way/maf/.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
index c9d00efc805..816b73de33f 100644
--- src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
+++ src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
@@ -71,30 +71,46 @@
 <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons28way/28way.mod"
 TARGET=_blank>vertebrate tree model</A> for this track was
 generated using the phyloFit program from the PHAST package  
 (REV model, EM algorithm, medium precision) using multiple alignments of 
 4-fold degenerate sites extracted from the 28way alignment
 (msa_view).  The 4d sites were derived from the 
 <A HREF="https://genome.crg.es/gencode/" TARGET=_blank>
 Oct 2005 Gencode Reference Gene set</A>,
 which was filtered to select single-coverage long transcripts.  A second, 
 <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons28way/placental.mod" 
 TARGET=_blank>
 mammalian tree model</A> including only placental mammals was used
 to generate the placental mammal conservation scoring.
 </P>
 
+<h2>Data Access</h2>
+<p>
+The conservation scores can be retrieved for a single region or for a list of regions with the
+<a href="hgTables?db=hg18&amp;hgta_group=compGeno&amp;hgta_track=phyloPCons28way">Table
+Browser</a>, and joined with other annotations in the <a href="hgIntegrator?db=hg18">Data
+Integrator</a>. For automated access, they are also served by our <a
+href="../goldenPath/help/api.html">REST API</a>.
+</p>
+<p>
+The files behind this track can be downloaded from our download server:
+<ul>
+  <li><a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg18/phyloP28way/"
+  target="_blank">PhyloP conservation scores</a></li>
+</ul>
+</p>
+
 <H2>Credits</H2>
 <P> This track was created using phyloP, phyloFit, and other programs in PHAST by 
 <A HREF="https://siepellab.labsites.cshl.edu/"
 TARGET=_blank>Adam Siepel's group</A> at Cold Spring Harbor Laboratory (original development
 done at the Haussler lab at UCSC).
 </P>
 <P>The phylogenetic tree is based on Murphy <EM>et al</EM>. (2001) and general 
 consensus in the vertebrate phylogeny community as of March 2007.
 </P>
 
 <H2>References</H2>
 <P>
 Siepel A, Pollard KS, Haussler D. 
 <A href="https://link.springer.com/chapter/10.1007/11732990_17" TARGET=_blank>
 New methods for detecting lineage-specific selection.</A>