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/cons241way.html src/hg/makeDb/trackDb/human/hg38/cons241way.html index 3d0c595af0b..8bab4fe9131 100644 --- src/hg/makeDb/trackDb/human/hg38/cons241way.html +++ src/hg/makeDb/trackDb/human/hg38/cons241way.html @@ -1,21 +1,15 @@ -<p> -Downloads for data in this track are available: -<ul> -<li> -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/">Cactus alignments</a> (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format) -</ul> <h2>Description</h2> <p><b>Warning:</b> Unlike other alignment tracks on the genome browser, this one does not show insertions in the query genomes. Also, all other alignment tracks show one query genome sequence for each target genome sequence, but in this track, each target genome sequence can be aligned to multiple query genome sequences. Only the first sequence is shown on the genome browser itself, the others are shown on the details page, when one clicks on the alignment. If you are interested in this track and want these shortcomings to be fixed, please contact us. </p> <p> This track shows multiple alignments of 241 vertebrate species and measurements of evolutionary conservation @@ -2389,30 +2383,58 @@ </p> <h3> PhyloP Conservation </h3> <p> The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (<a href="http://compgen.cshl.edu/phast/" target="_blank"> http://compgen.cshl.edu/phast/</a>). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). </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&hgta_group=compGeno&hgta_track=cons241way">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/cactus241way/" target="_blank">Cactus alignments</a> (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig 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>References</h2> <h3>Zoonomia:</h3> <p> Zoonomia Consortium.. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177664" target="_blank"> A comparative genomics multitool for scientific discovery and conservation</a>. <em>Nature</em>. 2020 Nov;587(7833):240-245. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177664" target="_blank">33177664</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759459/" target="_blank">PMC7759459</a>; DOI: <a href="https://doi.org/10.1038/s41586-020-2876-6" target="_blank">10.1038/s41586-020-2876-6</a> </p>