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
@@ -1,63 +1,63 @@
 <H2>Description</H2>
 
 <P>This track shows locations of the Single Nucleotide Polymorphisms
 on the Affymetrix 120K SNP Genotyping Array.  The SNPs in this track
 include all of the markers from the array that have been successfully
 mapped against the current assembly.</P>
 
 <P>The SNPs were selected from public domain databases or the Perlegen
 SNP database. Genotypes for these markers were generated at Affymetrix
 using GeneChip(r) DNA analysis technology.</P>
 
 <P>During sample preparation, an <B>enzyme</B> is used to fragment the
 genomic DNA into smaller pieces.  The restriction endonucleases
 <I><B>HindIII</B></I> and <I><B>XbaI</B></I> have been used to generate this
 data.</P>
 
 <P>Genotypes are reported as pairs of basecalls representing the two
 observed alleles.  Individual genotypes for which no call was made are
 labeled 'NC'.  A minimum of 46 genotype calls in the set of 54
 individuals are included for each SNP.</P>
 
 <P><B>Allele Frequency</B> for the 'A' allele is two times the number
 of 'AA' calls plus the number of 'AB' calls, divided by two times the
 total number of calls.  Allele Frequency for the 'B' allele is two
 times the number of 'BB' calls plus the number of 'AB' calls, divided
 by two times the total number of calls.  The <B>Minimum Allele
 Frequency</B> is the lesser of these two values.
 <B>Heterozygosity</B> is two times the product of the two allele
 frequencies.</P>
 
 <H2>Credits</H2>
 
 <P>Thanks to <A HREF="https://www.ncbi.nlm.nih.gov/SNP">dbSnp</A> at the
 NCBI for providing the public SNPs, and thanks to <A
 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>