Description: Some PDFs were removed and have to be downloaded from the upstream website instead.
Origin: vendor : Debian
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@@ -25,11 +25,11 @@
     detect similarity, then the PROmer program can generate alignments
     based upon the six-frame translations of both input sequences. The
     original MUMmer system, version 1.0, is described in our <a
-    href=MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
+    href="http://mummer.sourceforge.net/MUMmer.pdf">1999 <em>Nucleic Acids Research</em> paper</a>.
     Version 2.1 appeared a few years later and is described in our <a
-    href=MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
+    href="http://mummer.sourceforge.net/MUMmer2.pdf">2002 <em>Nucleic Acids Research</em> paper</a>,
     while MUMmer 3.0 was recently described in our <a
-    href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. We have also developed a GPU accelerated version of MUMmer called <a href="http://mummergpu.sf.net">MUMmerGPU</a>.</p>
+    href="http://mummer.sourceforge.net/MUMmer3.pdf">2004 <em>Genome Biology</em> paper</a>. We have also developed a GPU accelerated version of MUMmer called <a href="http://mummergpu.sf.net">MUMmerGPU</a>.</p>
 
 <p> For more
     information regarding the MUMmer package, please refer to the:</p>
@@ -174,7 +174,7 @@
   <h3><em><font color="#CC0000"> Applications </font></em></h3>
   <p>MUMmer 1 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
+    inversions, reported in this <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
@@ -229,14 +229,14 @@
   <p><a href="manual">MUMmer 3 user manual</a></p>
   <p><a href="examples">MUMmer 3 examples</a></p>
   <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
