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alignment.html
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alignment.html
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<!--
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>