089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/opossum/multiz5way.html src/hg/makeDb/trackDb/opossum/multiz5way.html
index 80d1c4cd9fd..dc634b53f40 100644
--- src/hg/makeDb/trackDb/opossum/multiz5way.html
+++ src/hg/makeDb/trackDb/opossum/multiz5way.html
@@ -87,32 +87,31 @@
 
 <H2>References</H2>
 
 <H3>Phylo-HMMs and phastCons:</H3>
 <P>
 Felsenstein J, Churchill GA.
 <A HREF="https://academic.oup.com/mbe/article/13/1/93/1055515"
 TARGET=_blank>A Hidden Markov Model approach to
 variation among sites in rate of evolution</A>.
 <em>Mol Biol Evol</em>. 1996 Jan;13(1):93-104.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8583911" target="_blank">8583911</a>
 </p>
 
 <P>
 Siepel A, Haussler D.
-<A HREF="http://compgen.cshl.edu/~acs/phylohmm.pdf"
-TARGET=_blank>Phylogenetic Hidden Markov Models</A>.
+Phylogenetic Hidden Markov Models.
 In: Nielsen R, editor. Statistical Methods in Molecular Evolution.
 New York: Springer; 2005. pp. 325-351.
 </P>
 
 <P>
 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,
 Clawson H, Spieth J, Hillier LW, Richards S, <EM>et al.</EM>
 <A HREF="https://genome.cshlp.org/content/15/8/1034"
 TARGET=_blank>Evolutionarily conserved elements in vertebrate, insect, worm,
 and yeast genomes</A>.
 <em>Genome Res</em>. 2005 Aug;15(8):1034-50.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16024819" target="_blank">16024819</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182216/" target="_blank">PMC1182216</a>
 </p>