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/regenRn1/cons7way.html src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
index 0db32ff0d3f..5b99b453ac1 100644
--- src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
+++ src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
@@ -49,40 +49,30 @@
 level (see <EM>Gap Annotation</EM>, below). </P>
 <P>
 <BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">
 <TR ALIGN=left><TH>Organism</TH><TH>Species</TH><TH>Release date</TH><TH>UCSC version</TH><TH>alignment type</TH></TR>
 <TR ALIGN=left><TD>Regeneron rat v1</TD><TD>Rattus norvegicus</TD><TD>May. 2019</TD><TD><A HREF="../cgi-bin/hgGateway?db=regenRn1" TARGET=_blank>Regeneron rat v1/regenRn1</A></TD><TD>reference species</TD></TR>
 <TR ALIGN=left><TD>Mouse</TD><TD>Mus musculus</TD><TD>Dec. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=mm10" TARGET=_blank>GRCm38/mm10</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Rabbit</TD><TD>Oryctolagus_cuniculus</TD><TD>Apr. 2009</TD><TD><A HREF="../cgi-bin/hgGateway?db=oryCun2" TARGET=_blank>Broad/oryCun2</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD>Dec. 2013</TD><TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg38" TARGET=_blank>GRCh38/hg38</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Crab eating macaque</TD><TD>Macaca fascicularis</TD><TD>Jun. 2013</TD><TD><A HREF="../cgi-bin/hgGateway?db=macFas5" TARGET=_blank>Macaca_fascicularis_5.0/macFas5</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>pig</TD><TD>Sus scrofa</TD><TD>Feb. 2017</TD><TD><A HREF="../cgi-bin/hgGateway?db=susScr11" TARGET=_blank>Sscrofa11.1/susScr11</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Dog</TD><TD>Canis lupus familiaris</TD><TD>Sep. 2011</TD><TD><A HREF="../cgi-bin/hgGateway?db=canFam3" TARGET=_blank>Broad CanFam3.1/canFam3</A></TD><TD>Syntenic net</TD></TR>
 </TABLE><BR>
 <B>Table 1.</B> <EM>Genome assemblies included in the 7-way Conservation track.</EM>
 </BLOCKQUOTE></P>
 
-Downloads for data in this track are available:
-<UL>
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/regenCho1/multiz7way/">Multiz alignments</A> (MAF format), and phylogenetic trees
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/regenCho1/phyloP7way/">PhyloP conservation</A> (WIG format)
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/regenCho1/phastCons7way/">PhastCons conservation</A> (WIG format)
-</UL>
-
 <H2>Display Conventions and Configuration</H2>
 <P>
 The track configuration options allow the user to display the three different
 sets of scores, all, birds or vertebrate, individually or all simultaneously.
 In full and pack display modes, conservation scores are displayed as a
 <EM>wiggle track</EM> (histogram) in which the height reflects the
 value of the score.
 The conservation wiggles can be configured in a variety of ways to
 highlight different aspects of the displayed information.
 Click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html"
 TARGET=_blank>Graph configuration help</A> link for an explanation
 of the configuration options.</P>
 <P>
 Pairwise alignments of each species to the $organism genome are
 displayed below the conservation histogram as a grayscale density plot (in
@@ -294,30 +284,61 @@
 <h3> Conserved Elements </h3>
 <P>
 The conserved elements were predicted by running phastCons with the
 --viterbi option.  The predicted elements are segments of the alignment
 that are likely to have been "generated" 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 "score" 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 "name" field and can be seen on the
 details page or in the browser when the track's display mode is set to
 "pack" or "full".
 </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=regenRn1&amp;hgta_group=compGeno&amp;hgta_track=cons7way">Table Browser</a>,
+which returns the alignments in MAF format and the scores as wiggle data. The conservation
+scores, though not the alignments, can also be joined with other annotations in the <a
+href="hgIntegrator?db=regenRn1">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/regenCho1/multiz7way/" target="_blank">Multiz alignments</A> (MAF format), and phylogenetic trees
+<LI>
+<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/regenCho1/phyloP7way/" target="_blank">PhyloP conservation</A> (WIG format)
+<LI>
+<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/regenCho1/phastCons7way/" target="_blank">PhastCons conservation</A> (WIG format)
+</UL>
+</p>
+<p>
+Genome-wide alignment 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. 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 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