b9c41cec68f33aec1a64d8cc709af9afc15155fa
mspeir
  Fri Sep 25 22:49:03 2026 -0700
hg38 cons241way: point the phyloP tree model text at the directory, refs #34803

The link went to phyloP241way/hg38.phyloP241way.mod, which does not exist and
never has under that name. The models live in cactus241way/phyloP241way, and
there are three of them rather than one: a general model and separate chrX and
chrY models. Link the directory and say so.

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 01b6de0caa5..17271ed4fc4 100644
--- src/hg/makeDb/trackDb/human/hg38/cons241way.html
+++ src/hg/makeDb/trackDb/human/hg38/cons241way.html
@@ -2364,34 +2364,35 @@
 The <em>phyloP</em> are phylogenetic methods that rely
 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="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/phyloP241way/"
 target=_blank>all-species tree model</a> for this track was
 generated using the <em>phyloFit</em> program from the PHAST package
 (REV model, EM algorithm, medium precision) using multiple alignments of
 4-fold degenerate sites extracted from the 241-way alignment
 (msa_view).  The 4d sites were derived from the RefSeq (Reviewed+Coding) gene
 set, filtered to select single-coverage long transcripts.
 </p>
 <p>
 This same tree model was used in the phyloP calculations; however, the
-background frequencies were modified to maintain reversibility.
-The resulting tree model:
-<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP241way/hg38.phyloP241way.mod"
-target=_blank>all species</a>.
+background frequencies were modified to maintain reversibility. The resulting
+models are in the
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/phyloP241way/"
+target="_blank">phyloP241way download directory</a> as .mod files: a general
+model, plus separate models for chrX and chrY.
 </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>