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 @@ -1,110 +1,126 @@ <H2>Description</H2> <P> This track shows measures of evolutionary conservation generated using the <em>phyloP</em> (Phylogenetic P-Values) program from the <A HREF="http://compgen.cshl.edu/phast/" target=_BLANK> PHAST package</A>. Two measurements are provided: conservation across 28 species, and an alternative measurement restricted to the placental mammal subset (17 species plus human) of the multiple alignment. </P> <P> PhyloP differs from phastCons — which is used to produce the scores in the main Conservation track — in several key ways. The scores produced by phyloP reflect individual alignment columns, and do not take into account conservation at neighboring sites. As a result, the phyloP conservation plot has a less smooth appearance, with more "texture" at individual bases, than the phastCons plot. In addition, this property makes phyloP more appropriate than phastCons for evaluating signatures of selection at particular bases or classes of bases in the genome (e.g., all third codon positions). In addition, phyloP requires fewer assumptions than phastCons, by depending only on a model of neutral evolution, rather than on models of both neutral evolution and negative selection (conservation). Finally, rather than representing probabilities of negative selection and ranging between 0 and 1, the phyloP scores represent -log p-values under a null hypothesis of neutral evolution, and range from 0 to infinity (although in practice there is a maximum achievable value for any particular data set).</P> <P> See the Conservation track description for information about the multiple alignments used as the basis of these conservation measurements. </P> <H2>Display Conventions and Configuration</H2> <P> The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. For example, the <EM>windowing function</EM> option controls how scores are combined across sites, with averaging as the default. This will have a strong effect on how the plot appears when zoomed out. <P> Click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" TARGET=_blank>Graph configuration help</A> link for an explanation of the configuration options.</P> <H2>Methods</H2> <P> Conservation scoring was performed using the <em>phyloP</em> program from the PHAST package. PhyloP is a general method for computing p-values of conservation by comparing estimated numbers of substitutions along the branches of a phylogeny with the distribution expected under neutral evolution (Siepel, Pollard, and Haussler, 2006). 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., --subtree was not used). Alignment gaps were treated as missing data. </P> <P> PhyloP relies on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The <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> <em>Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06)</em>. 2006.</P> <P> Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. <A HREF="https://science.sciencemag.org/content/294/5550/2348" TARGET=_blank> Resolution of the early placental mammal radiation using Bayesian phylogenetics</A>. <EM>Science</EM>. 14 Dec 2001;294(5550):2348-51. </P>