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/joinedRmsk.html src/hg/makeDb/trackDb/joinedRmsk.html
index 6f49523d240..108e3baf006 100644
--- src/hg/makeDb/trackDb/joinedRmsk.html
+++ src/hg/makeDb/trackDb/joinedRmsk.html
@@ -6,33 +6,33 @@
 program, which screens DNA sequences
 for interspersed repeats and low complexity DNA sequences. The program
 outputs a detailed annotation of the repeats that are present in the
 query sequence (represented by this track), as well as a modified version
 of the query sequence in which all the annotated repeats have been masked
 (generally available on the
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html"
 target=_blank>Downloads</a> page). RepeatMasker uses a separately curated version of the 
 <a href="https://www.girinst.org/repbase/update/index.html"
 target=_blank>Repbase Update</a> repeat library from the
 <a href="https://www.girinst.org/" target=_blank>Genetic 
 Information Research Institute</a> (GIRI).
 Repbase Update is described in Jurka (2000) in the References section below.  </p>
 <p>
 Alternatively, RepeatMasker can use the new
-<a href="http://dfam.janelia.org/" target="_blank">Dfam</a> database of repeat profile HMMs.
+<a href="https://www.dfam.org/" target="_blank">Dfam</a> database of repeat profile HMMs.
 Profile HMMs provide a richer description of the repeat families and when used with
-RepeatMasker + <a href="http://hmmer.janelia.org/" target="_blank">nhmmer</a> provide a more
+RepeatMasker + <a href="https://hmmer.org/" target="_blank">nhmmer</a> provide a more
 sensitive approach to identifying repeats. Dfam is described in Wheeler <em>et al</em>. (2012)
 in the References section below.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 
 <p>
 In dense display mode, a single line is displayed denoting the coverage of repeats using a series
 of black boxes.  
 </p>
 <p>
 In full display mode, the track view is controlled by the scale of the view.  At scales between 10 Mb
 and 30 kb, this track displays up to ten different classes of repeats (see below) one class per
 line. The repeat ranges are denoted as grayscale boxes, reflecting both the size of the repeat and
 the amount of base mismatch, base deletion, and base insertion associated with a repeat element.