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/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html
index 4679c0ab829..059491a172b 100644
--- src/hg/makeDb/trackDb/refSeqComposite.html
+++ src/hg/makeDb/trackDb/refSeqComposite.html
@@ -276,31 +276,31 @@
 -chrom=chr16 -start=34990190 -end=36727467 stdout</tt></p>
 <p>
 You can download a GTF format version of the RefSeq All table from the 
 <a href="http://hgdownload.soe.ucsc.edu/goldenPath/$db/bigZips/genes/">GTF downloads directory</a>.
 The genePred format tracks can also be converted to GTF format using the
 <tt>genePredToGtf</tt> utility, available from the
 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"
 target="_blank">utilities directory</a> on the UCSC downloads 
 server. The utility can be run from the command line like so:</p>
 <tt>genePredToGtf $db ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf</tt>
 <p>
 Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore 
 must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access
 section.</p>
 <p>
-A file containing the RNA sequences in <a href="http://genetics.bwh.harvard.edu/pph/FASTA.html" 
+A file containing the RNA sequences in <a href="http://genetics.bwh.harvard.edu/pph2/" 
 target="_blank">FASTA</a> format for all items in the <em>RefSeq All</em>, <em>RefSeq Curated</em>, 
 and <em>RefSeq Predicted</em> tracks can be found on our downloads server
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/ncbiRefSeq/seqNcbiRefSeq.rna.fa"
 target="_blank">here</a>.</p>
 <p>
 Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"
 target="_blank">mailing list archives</a> for questions.</p>
 
 <p>
 Previous versions of the ncbiRefSeq set of tracks can be found on our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/ncbiRefSeq">archive download server</a>.
 </p>
 
 <h2>Credits</h2>
 <p>
 This track was produced at UCSC from data generated by scientists worldwide and curated by the