1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
|
Description: Some PDFs were removed and have to be downloaded from the upstream website instead.
Origin: vendor : Debian
Forwarded: not-needed
--- a/docs/web/index.html
+++ b/docs/web/index.html
@@ -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
|
