-
Notifications
You must be signed in to change notification settings - Fork 16
/
alignment.html
149 lines (123 loc) · 7.35 KB
/
alignment.html
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
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
<!--
University of Freiburg WS 2017/2018
Chair for Bioinformatics
Supervisor: Martin Raden
Author: Alexander Mattheis
Hint: Some algorithms, structures and formats:
- Feng-Doolittle (NW version)
- Gotoh (with PAM- and BLOSSUM-matrices)
- Needleman-Wunsch (with PAM- and BLOSSUM-matrices)
- Newick format (different type)
- Sum-of-Pairs score (non-affine)
- UPGMA/WPGMA
have been also already been programmed before with Python
in the project Algorithms for Bioninformatics by Daniel Maticzka and Omer Alkhnbashi.
Hint 2: Look into the import-hints below, if you upload this project on a server.
Alexander Mattheis 2017-12-15
-->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Bioinformatics Algorithms</title>
<link rel="stylesheet"
type="text/css" href="http://rna.informatik.uni-freiburg.de/resources/corporate-design.css"/> <!-- stylesheet of RNA-Freiburg online -->
<!-- <link rel="stylesheet" type="text/css" href="css/corporate-design.css"/> <!-- stylesheet of RNA-Freiburg offline -->
<link rel="stylesheet" href="css/inner_style.css"> <!-- stylesheet for single pages -->
<link rel="stylesheet" href="css/outer_style.css"> <!-- stylesheet for offline usage -->
<!-- CONFIGURATION -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]},
displayAlign: "left"
});
</script> <!-- stores MathJax LaTeX-settings -->
<!-- THIRD PARTY LIBS -->
<script src="js/libs/FileSaver.min.js"></script> <!-- allows to save files on the desktop -->
<script src="js/libs/knockout-3.4.2.js"></script> <!-- to easify dynamic UI creation -->
<script src="js/libs/jquery.js"></script> <!-- to traverse and transform HTML -->
<script type="text/javascript" async
src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML">
</script> <!-- to display LaTeX formulas online -->
<!-- <script type="text/javascript" src="MathJax/MathJax.js?config=TeX-MML-AM_CHTML"></script> <!-- to display LaTeX formulas offline -->
<script src="js/libs/namespace.js"></script> <!-- to create namespaces -->
<script type="text/javascript" src="js/libs/raphael-min.js"></script> <!-- SVG-rendering library for phylogenetic trees -->
<script type="text/javascript" src="js/libs/jsphylosvg.js"></script> <!-- to draw phylogenetic trees -->
<!-- IO -->
<script src="js/interfaces/dropdown_menu.js"></script> <!-- allows to choose an algorithm for loading -->
<script src="js/interfaces/interface.js"></script> <!-- superclass for all interfaces -->
<script src="js/interfaces/alignment_interface.js"></script> <!-- superclass for all interfaces of alignment algorithms -->
<script src="js/interfaces/clustering_interface.js"></script> <!-- superclass for all interfaces of clustering algorithms -->
<script src="js/interfaces/linear_alignment_interface.js"></script> <!-- stores viewmodels and interface functions of linear alignment algorithms -->
<script src="js/interfaces/multi_sequence_interface.js"></script> <!-- stores viewmodels and interface functions of multi-sequence algorithms -->
<script src="js/interfaces/subadditive_alignment_interface.js"></script> <!-- stores viewmodels and interface functions of subadditive alignment algorithms -->
<!-- CONTROLS "LOGIC" -->
<script src="js/defaults.js"></script> <!-- stores all globally used constants -->
<script src="js/loader.js"></script> <!-- loads algorithms into the alignment.html -->
<!-- formats -->
<script src="js/formats/csv_parser.js"></script> <!-- allows to read and write csv data -->
<script src="js/formats/newick_encoder.js"></script> <!-- allows to encode a binary tree in a newick string -->
<!-- post processing -->
<script src="js/post_processing/input_processor.js"></script> <!-- does the post-processing of inputs -->
<script src="js/post_processing/visualizer.js"></script> <!-- contains all functions for visualization -->
<!-- ALGORITHMS "LOGIC" -->
<script src="js/bases/alignment.js"></script> <!-- stores basic alignment functions -->
<script src="js/bases/multi_sequence_alignment.js"></script> <!-- stores basic multi-sequence alignment functions -->
<script src="js/bases/clustering.js"></script> <!-- stores basic clustering functions -->
<!-- IMPORT HINTS: The following algorithms are also loaded by the loader!
This can lead to problems i.e. if you load "Needleman-Wunsch",
then remove the import "js/needleman_wunsch.js" before you load the algorithm with the loader or Knockout may fail!
Probably deactivate the reinitialize()-function in the loader.
So, never load the same resource twice. Therefore have also a look in the imports of the interface classes
if something goes wrong! -->
<script src="js/agglomerative_clustering.js"></script> <!-- stores agglomerative clustering algorithms -->
<script src="js/feng_doolittle.js"></script> <!-- stores Feng-Doolittle algorithm -->
<script src="js/gotoh.js"></script> <!-- stores Gotoh algorithm -->
<script src="js/gotoh_local.js"></script> <!-- stores Gotoh (Local) algorithm -->
<script src="js/needleman_wunsch.js"></script> <!-- stores Needleman-Wunsch algorithm -->
<script src="js/neighbour_joining.js"></script> <!-- stores Neighbour-Joining algorithm -->
<script src="js/smith_waterman.js"></script> <!-- stores Smith-Waterman algorithm -->
</head>
<body>
<header>
<div class="logo">
<a href="alignment.html">
<h5>Bioinformatics Algorithms</h5>
</a>
</div>
</header>
<div id="overlay"></div>
<div id="page_contents">
<nav id="top_bar">
<div id="algorithm_chooser">
<div class="dropdown_button"></div>
</div>
<div id="algorithm_display">Choose algorithm...</div>
</nav>
<div id="algorithm_menu">
<ul>
<li><a href="#">Agglomerative Clustering</a></li>
<li><a href="#">Arslan-Eğecioğlu-Pevzner</a></li>
<li><a href="#">Feng-Doolittle</a></li>
<li><a href="#">Gotoh</a></li>
<li><a href="#">Gotoh (Local)</a></li>
<li><a href="#">Hirschberg</a></li>
<li><a href="#">Iterative Refinement</a></li>
<li><a href="#">Needleman-Wunsch</a></li>
<li><a href="#">Notredame-Higgins-Heringa</a></li>
<li><a href="#">Smith-Waterman</a></li>
<li><a href="#">Waterman-Smith-Beyer</a></li>
</ul>
</div>
<div id="algorithm_view"></div>
</div>
<footer>
<span>
Author: Alexander Mattheis
</span>
<span>
Supervised by <a href="http://www.bioinf.uni-freiburg.de"/>Martin Raden</a>
</span>
</footer>
</body>
</html>