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/drosophila/netDp3.html src/hg/makeDb/trackDb/drosophila/netDp3.html
index 251033ec693..781f89b1b95 100644
--- src/hg/makeDb/trackDb/drosophila/netDp3.html
+++ src/hg/makeDb/trackDb/drosophila/netDp3.html
@@ -43,31 +43,31 @@
 highest-scoring chains in the genome ranked first. The program
 chainNet was then used to place the chains one at a time, trimming them as 
 necessary to fit into sections not already covered by a higher-scoring chain. 
 During this process, a natural hierarchy emerged in which a chain that filled 
 a gap in a higher-scoring chain was placed underneath that chain. The program 
 netSyntenic was used to fill in information about the relationship between 
 higher- and lower-level chains, such as whether a lower-level
 chain was syntenic or inverted relative to the higher-level chain. 
 The program netClass was then used to fill in how much of the gaps and chains 
 contained <em>N</em>s (sequencing gaps) in one or both species and how much
 was filled with transposons inserted before and after the two organisms 
 diverged.</P>
 
 <H2>Credits</H2>
 <P>
-The dp3 data were obtained from the <A HREF="http://flybase.org/" 
+The dp3 data were obtained from the <A HREF="https://flybase.org/" 
 TARGET=_blank>FlyBase</A> Release 1.0 assembly.</P>
 <P>
 The chainNet, netSyntenic, and netClass programs were
 developed at the University of California
 Santa Cruz by Jim Kent.</P>
 <P>
 Blastz was developed at <A HREF="http://www.bx.psu.edu/miller_lab/"
 TARGET=_blank>Pennsylvania State University</A> by
 Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from
 Ross Hardison.</P>
 <P>
 Lineage-specific repeats were identified by Arian Smit and his program 
 <A HREF="https://www.repeatmasker.org/" TARGET=_blank>RepeatMasker</A>.</P>
 <P>
 The browser display and database storage of the nets were made