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/human/encodeEgaspSuper.html src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
index 93bd5b11e13..e58f8692895 100644
--- src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
+++ src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
@@ -17,31 +17,31 @@
 The <B>EGASP Update</B> track shows gene predictions that cover
 all ENCODE regions, submitted after the GENCODE release.
 <P>
 These annotations were originally produced using the hg17 assembly. </P>
 <P>
 The following gene predictions are included:
 <UL>
 <LI>
 <A HREF="http://hollywood.mit.edu/acescan/" TARGET=_blank>ACEScan</A></LI>
 <LI>
 <A HREF="https://www.ncbi.nlm.nih.gov/ieb/research/acembly/"
 TARGET=_blank>AceView</A></LI>
 <LI>
 DOGFISH-C</LI>
 <LI>
-<A HREF="http://www.ensembl.org" TARGET=_blank>Ensembl</A></LI>
+<A HREF="https://www.ensembl.org" TARGET=_blank>Ensembl</A></LI>
 <LI>
 <A HREF="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s7"
 TARGET=_blank>Exogean</A></LI>
 <LI>
 <A HREF="http://compbio.fmph.uniba.sk/exonhunter/"
 TARGET=_blank>ExonHunter</A></LI>
 <LI>
 <A HREF="http://linux1.softberry.com/berry.phtml" TARGET=_blank>Fgenesh Pseudogenes</A></LI>
 <LI>
 <A HREF="http://linux1.softberry.com/berry.phtml" TARGET=_blank>Fgenesh++</A></LI>
 <LI>
 <A HREF="https://genome.crg.es/software/geneid/index.html"
 TARGET=_blank>GeneID-U12</A> </LI>
 <LI>
 <A HREF="http://opal.biology.gatech.edu/GeneMark/"