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/phyloPConsLs44way.html src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html index 12d6dcb251b..22e74bf2692 100644 --- src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html +++ src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html @@ -1,70 +1,86 @@ <H2>Description</H2> <P> This track shows basewise measurements of evolutionary conservation/acceleration in particular clades of interest, <em>relative </em> to the levels of conservation/acceleration displayed elsewhere in the phylogeny. These scores were produced by the <em>phyloP</em> program from the <A TARGET=_BLANK HREF="http://compgen.cshl.edu/phast/"> PHAST package</A> , using the same species set, multiz alignment, and neutral model of evolution that were used for the main conservation track (see description page for "Vertebrate Multiz Alignment & Conservation (44 Species)" track for details). The individual scores represent -log p-values for a slow-down or speed-up in the estimated evolutionary rate for the clade of interest, relative to the estimated rate outside that clade, under a null hypothesis of neutral evolution (see Methods). </P> <P> As with the phyloP scores for the main conservation track, positive values indicate a decrease in rate (conservation) and negative values indicate an increase in rate (acceleration). In this case, however, the score measures a <em>change</em> in evolutionary rate in a clade of interest, possibly indicating clade-specific selection rather than the absolute rate across the phylogeny. Note that this track does not attempt to distinguish between negative and positive directional selection. For example, a clade-specific increase in rate could be due to clade-specific positive selection or relaxation of constraint. Similarly, a clade-specific decrease in rate could be due to gain of negative selection or loss of positive selection. </P> <H2>Methods</H2> <P> The scores were produced by running <em>phyloP</em> with the options --method LRT --mode CONACC --wig-scores, and by indicating the clade of interest with the --subtree option (see PHAST docs <a href="http://compgen.cshl.edu/phast/" target="_blank"> http://compgen.cshl.edu/phast/</a>). The program was given a neutral model estimated from fourfold degenerate sites, as decribed for the main conservation track. With these options, <em>phyloP</em> performs a likelihood ratio test at each alignment column. This test compares a null model in which the neutral branch lengths are all scaled by a single scaling factor (a free parameter, estimated by maximum likelihood), and an alternative model with separate scaling factors for the clade of interest and the remainder of the phylogeny (both estimated by maximum likelihood). To obtain an approximate p-value, the log likelihood ratio of these two hypotheses is compared to an asymptotic chi-squared null distribution, in the usual way. Scores are then computed as -log 10 p-values. If the estimated rate for the clade of interest is greater than the estimated rate outside that clade, the score is negated, to indicate acceleration rather than conservation. </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=phyloPConsLs44way">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/phyloP44way/" + target="_blank">PhyloP conservation scores</a></li> +</ul> +</p> <H2>References</H2> <P> Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, and Haussler D. <a href="http://www.nature.com/nature/journal/v443/n7108/abs/nature05113.html" target="_blank">An RNA gene expressed during cortical development evolved rapidly in humans.</a> Nature. 443:167-172, 2006. </P> <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> Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06)/. 2006. </P>