5fc81fc9aeef72ee718678ce93da39337b2db6fe
markd
  Tue Dec 3 19:50:33 2024 -0800
fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references

diff --git src/hg/makeDb/trackDb/humanChainNet.html src/hg/makeDb/trackDb/humanChainNet.html
index aa57406..4e353cf 100644
--- src/hg/makeDb/trackDb/humanChainNet.html
+++ src/hg/makeDb/trackDb/humanChainNet.html
@@ -102,53 +102,59 @@
 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>
-Lastz (previously known as 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>
+LASTZ was developed at
+<A HREF="http://www.bx.psu.edu/~rsharris/lastz/" TARGET=_blank>Miller Lab at Pennsylvania State University</A> by 
+Bob Harris.
+</P>
 <P>
 Lineage-specific repeats were identified by Arian Smit and his 
 <A HREF="https://www.repeatmasker.org/" TARGET=_blank>RepeatMasker</A>
 program.</P>
 <P>
 The axtChain program was developed at the University of California at 
 Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>
 <P>
 The browser display and database storage of the chains and nets were created
 by Robert Baertsch and Jim Kent.</P>
 <P>
 The chainNet, netSyntenic, and netClass programs were
 developed at the University of California
 Santa Cruz by Jim Kent.</P>
 <P>
 
 <H2>References</H2>
 <P>
+Harris RS.
+<a href="http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf"
+target="_blank">Improved pairwise alignment of genomic DNA</a>.
+<em>Ph.D. Thesis</em>. Pennsylvania State University, USA. 2007.
+</P>
+
+<P>
 Chiaromonte F, Yap VB, Miller W. 
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928468&dopt=Abstract" 
 TARGET=_blank>Scoring pairwise genomic sequence alignments</A>. 
 <em>Pac Symp Biocomput.</em> 2002;:115-26.</P>
 <P>
 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
 <A HREF="http://www.pnas.org/cgi/content/abstract/1932072100v1" 
 TARGET=_blank>Evolution's cauldron: Duplication, deletion, and rearrangement
 in the mouse and human genomes</A>.
 <em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.</P>
 <P>
 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
 Haussler D, Miller W.
 <A HREF="http://www.genome.org/cgi/content/abstract/13/1/103" 
 TARGET=_blank>Human-Mouse Alignments with BLASTZ</A>.