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/rat/rn6/cons20way.html src/hg/makeDb/trackDb/rat/rn6/cons20way.html
index 732011ec009..8fecffbf940 100644
--- src/hg/makeDb/trackDb/rat/rn6/cons20way.html
+++ src/hg/makeDb/trackDb/rat/rn6/cons20way.html
@@ -1,25 +1,15 @@
-<p>
-Downloads for data in this track are available:
-<ul>
-<li>
-<a href="http://hgdownload.soe.ucsc.edu/goldenPath/rn6/multiz20way/">Multiz alignments</a> (MAF format), and phylogenetic trees
-<li>
-<a href="http://hgdownload.soe.ucsc.edu/goldenPath/rn6/phyloP20way/">PhyloP conservation</a> (WIG format)
-<li>
-<a href="http://hgdownload.soe.ucsc.edu/goldenPath/rn6/phastCons20way/">PhastCons conservation</a> (WIG format)
-</ul>
 
 <h2>Description</h2>
 <p>
 This track shows multiple alignments of 20 species
 and measurements of evolutionary conservation using
 two methods (<em>phastCons</em> and <em>phyloP</em>) from the
 <a href="http://compgen.cshl.edu/phast/" target=_blank>
 PHAST package</a>, for all 20 species.
 The multiple alignments were generated using multiz and 
 other tools in the UCSC/<a href="http://www.bx.psu.edu/miller_lab/" 
 target=_blank>Penn State Bioinformatics</a>
 comparative genomics alignment pipeline.
 Conserved elements identified by phastCons are also displayed in
 this track.
 </p>
@@ -336,30 +326,62 @@
 <p>
 The conserved elements were predicted by running phastCons with the
 --most-conserved (aka --viterbi) option.  The predicted elements are
 segments of the alignment
 that are likely to have been &quot;generated&quot; by the conserved state of the
 phylo-HMM. Each element is assigned a log-odds score equal to its log
 probability under the conserved model minus its log probability under the
 non-conserved model. The &quot;score&quot; field associated with this track contains
 transformed log-odds scores, taking values between 0 and 1000. (The scores
 are transformed using a monotonic function of the form a * log(x) + b.) The
 raw log odds scores are retained in the &quot;name&quot; field and can be seen on the
 details page or in the browser when the track's display mode is set to
 &quot;pack&quot; or &quot;full&quot;.
 </p>
 
+<h2>Data Access</h2>
+<p>
+The alignments and the conservation scores can be retrieved for a single region or for a list of
+regions with the <a
+href="hgTables?db=rn6&amp;hgta_group=compGeno&amp;hgta_track=cons20way">Table Browser</a>, which
+returns the alignments in MAF format and the scores as wiggle data. The scores and the conserved
+elements, though not the alignments, can also be joined with other annotations in the <a
+href="hgIntegrator?db=rn6">Data Integrator</a>. For automated access, our <a
+href="../goldenPath/help/api.html">REST API</a> serves the alignment and conservation tracks
+individually, by name.
+</p>
+<p>
+Downloads for data in this track are available:
+<ul>
+<li>
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/rn6/multiz20way/" target="_blank">Multiz alignments</a> (MAF format), and phylogenetic trees
+<li>
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/rn6/phyloP20way/" target="_blank">PhyloP conservation</a> (WIG format)
+<li>
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/rn6/phastCons20way/" target="_blank">PhastCons conservation</a> (WIG format)
+</ul>
+</p>
+<p>
+Genome-wide alignment and conservation files are large. Among our command-line programs,
+<tt>mafsInRegion</tt>, <tt>mafSpeciesSubset</tt> and <tt>mafFrags</tt> pull out a region, a
+subset of species, or the alignment underlying a gene, and <tt>bigWigToWig</tt> and
+<tt>bigWigSummary</tt> read the conservation files. They can be downloaded from the <a
+href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">utilities directory</a>, and
+each one prints its usage when run with no arguments. See our <a
+href="../FAQ/FAQdownloads.html">Data Access FAQ</a> for more information.
+</p>
+
 <h2>Credits</h2>
 <p> This track was created using the following programs:
 <ul>
 <li> Alignment tools: lastz (formerly blastz) and multiz by Bob Harris, Minmei Hou, Scott Schwartz and Webb
 Miller of the <a href="http://www.bx.psu.edu/miller_lab/" 
 target=_blank>Penn State Bioinformatics Group</a>
 <li> Chaining and Netting:  axtChain, chainNet by Jim Kent at UCSC
 <li> Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and
 other programs in PHAST by 
 <a href="https://siepellab.labsites.cshl.edu/"
 target=_blank>Adam Siepel</a> at Cold Spring Harbor Laboratory (original development
 done at the Haussler lab at UCSC).
 <li> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows
 by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
 <li> Tree image generator: phyloPng by Galt Barber, UCSC