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--- docs/web/index.html.orig 2006-06-29 19:35:07.000000000 +0200
+++ docs/web/index.html 2007-05-07 14:07:52.000000000 +0200
@@ -125,7 +125,7 @@
<h3><em><font color="#CC0000"> Applications </font></em></h3>
<p>MUMmer 1.0 was used to detect numerous large-scale inversions in bacterial
genomes, leading to a new model of chromosome inversions, reported in this
- <a href=XFiles.pdf>2000 <em>Genome Biology</em> paper</a>. It was also used
+ <a href="http://mummer.sourceforge.net/XFiles.pdf">2000 <em>Genome Biology</em> paper</a>. It was also used
to discover evidence for a recent whole-genome duplication in <em>Arabidopsis
thaliana</em>, reported in "Analysis of the genome sequence of the flowering
plant <em>Arabidopsis thaliana</em>." The Arabidopsis Genome Initiative, <em>Nature</em>
@@ -177,14 +177,14 @@
<h3><a href="manual">MUMmer3.0 user manual</a></h3>
<h3><a href="examples">MUMmer3.0 examples</a></h3>
<p>Open source MUMmer 3.0 is described in "<a
- href=MUMmer3.pdf>Versatile and open software for comparing large genomes</a>."
+ href="http://mummer.sourceforge.net/MUMmer3.pdf">Versatile and open software for comparing large genomes</a>."
S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu,
and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
- <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=MUMmer2.pdf>Fast
+ <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href="http://mummer.sourceforge.net/MUMmer2.pdf">Fast
Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher,
A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em>
(2002), Vol. 30, No. 11 2478-2483.</p>
- <p>MUMmer 1.0 is described in "<a href=MUMmer.pdf>Alignment of Whole Genomes</a>."
+ <p>MUMmer 1.0 is described in "<a href="http://mummer.sourceforge.net/MUMmer.pdf">Alignment of Whole Genomes</a>."
A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L.
Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
<p>Space efficent suffix trees are described in "<a href=http://www.zbh.uni-hamburg.de/staff/kurtz/papers/Kur1999.pdf>Reducing
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