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/affy120K.html src/hg/makeDb/trackDb/human/affy120K.html
index 9a2043f72ac..e6b73e4dfc3 100644
--- src/hg/makeDb/trackDb/human/affy120K.html
+++ src/hg/makeDb/trackDb/human/affy120K.html
@@ -35,29 +35,29 @@
 HREF="http://www.perlegen.com">Perlegen Sciences, Inc.</A> for
 providing additional SNPs from their database.  Additional information
 about the Perlegen SNP discovery process can be found in 
 <a href="http://www.sciencemag.org/cgi/content/abstract/294/5547/1719">
 <i>Science</i> <b>294</b>: 1719-1723 (2001)</a>:
 <p>
 <b>Blocks of Limited Haplotype Diversity Revealed by High-Resolution
 Scanning of Human Chromosome 21</b>
 <br>
 N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett, J. M. Doshi,
 C. R. Hacker, C. R. Kautzer, D. H. Lee, C. Marjoribanks,
 D. P. McDonough,  B. T. N. Nguyen, M. C. Norris, J. B. Sheehan,
 N. Shen, D. Stern, R. P. Stokowski, D. J. Thomas, M. O. Trulson,
 K. R. Vyas, K. A. Frazer, S. P. A. Fodor, and D. R. Cox.
 
-<P>Thanks to <A HREF="http://www.affymetrix.com">Affymetrix, Inc.</A>
+<P>Thanks to <A HREF="https://www.affymetrix.com">Affymetrix, Inc.</A>
 for developing the genotyping array and providing the genotype data
 for 54 individuals.  For more details on this genotyping assay, please
 see the supplemental information on the <A
-HREF="http://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx">Affymetrix
+HREF="https://www.affymetrix.com/support/technical/sample_data/genotyping_data.affx">Affymetrix
 120K SNP</A> product.</P>
 
 <H2>Terms of Use</H2>
 <P>Please see the <A
 HREF="https://www.affymetrix.com:443/site/terms.affx">Terms and
 Conditions</A> for the use of this data at the <A
-HREF="http://www.affymetrix.com">Affymetrix, Inc.</A> site.</P>
+HREF="https://www.affymetrix.com">Affymetrix, Inc.</A> site.</P>