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/hg38/cons5way.html src/hg/makeDb/trackDb/human/hg38/cons5way.html
index 45070e52608..f4490bf2e24 100644
--- src/hg/makeDb/trackDb/human/hg38/cons5way.html
+++ src/hg/makeDb/trackDb/human/hg38/cons5way.html
@@ -47,40 +47,30 @@
 Missing sequence in the assemblies is highlighted in the track display
 by regions of yellow when zoomed out and Ns displayed at base
 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>Human</TD><TD>Homo sapiens</TD><TD>Dec. 2013</TD><TD><A HREF="../cgi-bin/hgGateway?db=hg38" TARGET=_blank>GRCh38/hg38</A></TD><TD>reference species</TD></TR>
 <TR ALIGN=left><TD>Malayan flying lemur</TD><TD>Galeopterus variegatus</TD><TD>Jun. 2014</TD><TD><A HREF="../cgi-bin/hgGateway?db=galVar1" TARGET=_blank>WashU 3.0.2/galVar1</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Chinese tree shrew</TD><TD>Tupia chinensis</TD><TD>Jan. 2013</TD><TD><A HREF="../cgi-bin/hgGateway?db=tupChi1" TARGET=_blank>BGI CR_1.0/tupChi1</A></TD><TD>Syntenic net</TD></TR>
 <TR ALIGN=left><TD>Guinea pig</TD><TD>Cavia porcellus</TD><TD>Feb. 2008</TD><TD><A HREF="../cgi-bin/hgGateway?db=cavPor3" TARGET=_blank>Broad/cavPor3</A></TD><TD>Syntenic net</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>
 </TABLE><BR>
 <B>Table 1.</B> <EM>Genome assemblies included in the 5-way Conservation track.</EM>
 </BLOCKQUOTE></P>
 
-Downloads for data in this track are available:
-<UL>
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz5way/">Multiz alignments</A> (MAF format), and phylogenetic trees
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP5way/">PhyloP conservation</A> (WIG format)
-<LI>
-<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons5way/">PhastCons conservation</A> (WIG format)
-</UL>
-
 <p>
 (UPDATE May 2015) Note that due to an error while creating the alignments for this
 track, some of the alignments are missing from some of the unplaced and unlocalized contigs
 in rhesus, mouse and dog. This problem has been fixed in the subsequent
 <a href=" ../../cgi-bin/hgTrackUi?db=hg38&g=cons20way">Primate Conservation</a>
 track and any future Conservation tracks.
 </p>
 
 <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.
@@ -298,30 +288,61 @@
 <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=hg38&amp;hgta_group=compGeno&amp;hgta_track=cons5way">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=hg38">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/hg38/multiz5way/" target="_blank">Multiz alignments</A> (MAF format), and phylogenetic trees
+<LI>
+<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP5way/" target="_blank">PhyloP conservation</A> (WIG format)
+<LI>
+<A HREF="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons5way/" 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: 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