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/genieAlt.html src/hg/makeDb/trackDb/genieAlt.html
index 1ea0fe81e2a..9d64ba8c742 100644
--- src/hg/makeDb/trackDb/genieAlt.html
+++ src/hg/makeDb/trackDb/genieAlt.html
@@ -1,5 +1,5 @@
 <H2>Description</H2>
 <P>Genie predictions are based on 
-<A HREF = "http://www.affymetrix.com" TARGET=_blank>Affymetrix's</A> 
+<A HREF = "https://www.affymetrix.com" TARGET=_blank>Affymetrix's</A> 
 Genie gene finding software.  Genie is a generalized HMM 
 which accepts constraints based on mRNA and EST data. </P>