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&hgta_group=compGeno&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>