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/affyAllExonProbes.html src/hg/makeDb/trackDb/affyAllExonProbes.html
index f7fdf022fe6..d11eb6b24ed 100644
--- src/hg/makeDb/trackDb/affyAllExonProbes.html
+++ src/hg/makeDb/trackDb/affyAllExonProbes.html
@@ -31,44 +31,44 @@
 on the <B>Affy Exon Tissue</B> track.</P>
 
 <H2>Credits and References</H2>
 <P>
 The exons interrogated by the probe sets displayed in this track are
 from the Affymetrix Exon 1.0 GeneChip and were derived from a
 number of sources. In addition to the millions of cDNA sequences
 contributed to the 
 <A HREF="https://www.ncbi.nlm.nih.gov/genbank/" 
 TARGET=_blank>GenBank</A>, 
 <A HREF="https://www.ncbi.nlm.nih.gov/dbEST/" TARGET=_blank>dbEst</A> and 
 <A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>RefSeq</A> 
 databases by
 individual labs and scientists, the following annotations were used:
 <P>
-<A HREF="http://www.ensembl.org/index.html" 
+<A HREF="https://www.ensembl.org/index.html" 
 TARGET=_blank><B>Ensembl</B></A><B>: </B>
 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T <em>et
 al</em>.
 <a href="https://academic.oup.com/nar/article/30/1/38/1332872" target="_blank">
 The Ensembl genome database project</a>.
 <em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>
 </p>
 
 <P>
 <a href="http://compgen.cshl.edu/phast/" target"_blank"><B>Exoniphy</a>:</B> Siepel, A., Haussler, D. 
-<A HREF="http://compgen.cshl.edu/~acs/recomb2004.pdf"
+<A HREF="https://doi.org/10.1101/gr.3715005"
 TARGET=_blank>Computational identification of evolutionarily conserved 
 exons</A>.
 <em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>, 
 177-186 (2004).
 </P>
 
 <P>
 <B><A HREF="https://genome.crg.es/geneid.html" TARGET=_blank>Geneid Genes</A>:</B>
 Parra G, Blanco E, Guig&#243; R.
 <a href="https://genome.cshlp.org/content/10/4/511.abstract" target="_blank">
 GeneID in Drosophila</a>.
 <em>Genome Res</em>. 2000 Apr;10(4):511-5.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10779490" target="_blank">10779490</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310871/" target="_blank">PMC310871</a>
 </p>