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15 <section ref="./mussagl_manual.html#features-to-be-implemented" />
17 <section ref="./mussagl_manual.html#introduction" title="Introduction">
18 <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
19 <section ref="./mussagl_manual.html#what-is-mussagl">About</section>
21 <section ref="./mussagl_manual.html#short-history-of-mussa" title="Short History of Mussa">
22 <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
23 <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
24 <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
27 <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
28 <section ref="./mussagl_manual.html#license" title="License"/>
29 <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
30 <section ref="./mussagl_manual.html#download" title="Download"/>
31 <section ref="./mussagl_manual.html#install" title="Install">
32 <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
33 <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
34 <section ref="./mussagl_manual.html#linux" title="Linux"/>
35 <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
38 <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
39 <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
40 <section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
41 <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
42 <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
43 <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
45 <section ref="./mussagl_manual.html#main-window" title="Main Window">
46 <section ref="./mussagl_manual.html#overview" title="Overview"/>
47 <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
48 <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
49 <section ref="./mussagl_manual.html#motif" title="Motif"/>
50 <section ref="./mussagl_manual.html#red-conservation-tracks" title="Red Conservation Tracks"/>
51 <section ref="./mussagl_manual.html#blue-conservation-tracks" title="Blue Conservation Tracks"/>
52 <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
53 <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
54 <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
55 <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
57 <section ref="./mussagl_manual.html#saving" title="Saving">
58 <section ref="./mussagl_manual.html#save-on-close" title="Save on close" />
59 <section ref="./mussagl_manual.html#save-analysis" title="Save Analysis" />
60 <section ref="./mussagl_manual.html#save-analysis-as" title="Save Analysis As" />
61 <section ref="./mussagl_manual.html#save-motif-list" title="Save Motif List" />
63 <section ref="./mussagl_manual.html#viewing-multiple-analyses" title="Viewing Multiple Analyses" />
64 <section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
65 <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
66 <section ref="./mussagl_manual.html#motifs" title="Motifs">
67 <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
68 <section ref="./mussagl_manual.html#save-motifs-to-file" title="Save Motifs to File"/>
69 <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog">
70 <section ref="./mussagl_manual.html#deleting-a-motif" title="Deleting a Motif" />
74 <section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
75 <section ref="./mussagl_manual.html#sub-analysis" title="Sub-analysis" />
76 <section ref="./mussagl_manual.html#copying-sequence-to-clipboard" title="Copying sequence to clipboard" />
77 <section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
78 <section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
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81 <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
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86 <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
87 <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
89 <section ref="./mussagl_manual.html#obtaining-input-data-continued" title="Obtaining Input Data - Continued">
90 <section ref="./mussagl_manual.html#ucsc-genome-browser-method" title="UCSC Genome Browser Method" >
91 <section ref="./mussagl_manual.html#step-1-find-smn1" title="Step 1 - Find SMN1"/>
92 <section ref="./mussagl_manual.html#step-2-download-cds-utr-sequence-for-annotations" title="Step 2 - Download CDS/UTR sequence for annotations"/>
93 <section ref="./mussagl_manual.html#step-3-download-gene-and-upstream-downstream-sequence" title="Step 3 - Download gene and upstream/downstream sequence"/>
94 <section ref="./mussagl_manual.html#step-4-same-similar-related-gene-other-species" title="Step 4 - Same/similar/related gene other species."/>
95 <section ref="./mussagl_manual.html#step-5-create-analysis" title="Step 5 - Create Analysis"/>
98 <section ref="./mussagl_manual.html#understanding-mussa" title="Understanding Mussa"/>
99 <section ref="./mussagl_manual.html#command-line" title="Command Line"/>
100 <section ref="./mussagl_manual.html#performance" title="Performance">
101 <section ref="./mussagl_manual.html#algorithm-behavior" title="Algorithm Behavior"/>
102 <section ref="./mussagl_manual.html#repeats" title="Repeats"/>
104 <section ref="./mussagl_manual.html#details" title="Details">
105 <section ref="./mussagl_manual.html#case-conservation-track-suddenly-stops" title="Case: Conservation track suddenly stops"/>
107 <section ref="./mussagl_manual.html#python-interpreter" title="Python Interpreter"/>
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