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/mouse/altSeqComposite.html src/hg/makeDb/trackDb/mouse/altSeqComposite.html
index 0b9610b..e879877 100644
--- src/hg/makeDb/trackDb/mouse/altSeqComposite.html
+++ src/hg/makeDb/trackDb/mouse/altSeqComposite.html
@@ -154,58 +154,62 @@
 <h3>Net Track</h3>
 
 <p>
 Chains were derived from lastz alignments, using the methods described in the chain track description
 above, and sorted with the 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 sequences 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>
-
+<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 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>
 
 <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/pubmed/11928468" 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/content/100/20/11484.abstract" 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>