--- /dev/null
+<!DOCTYPE DCF>
+<assistantconfig version="3.2.0">
+
+ <profile>
+ <property name="name">mussaglmanual</property>
+ <property name="title">Mussagl Manual</property>
+ <property name="applicationicon">images/handbook.png</property>
+ <property name="startpage">mussagl_manual.html</property>
+ <property name="aboutmenutext">About Mussagl Manual</property>
+ <property name="abouturl">about.txt</property>
+ <property name="assistantdocs">.</property>
+ </profile>
+
+ <DCF ref="mussagl_manual.html" icon="handbook.png" imagedir="../img/"
+ title="Mussagl Manual">
+
+ <section ref="./mussagl_manual.html#contents" title="Contents" />
+
+ <section ref="./mussagl_manual.html#introduction" title="Introduction">
+ <section ref="./mussagl_manual.html#what-is-mussagl" title="What is Mussagl?">
+ <keyword ref="./chap1/section1.html#foo">foo</keyword>
+ <keyword ref="./chap1/section1.html#bla">bla</keyword>
+ <section ref="./mussagl_manual.html#mussa-python-pmw-prototype" title="Mussa Python/PMW Prototype"/>
+ <section ref="./mussagl_manual.html#mussa-c-fltk" title="Mussa C++/FLTK"/>
+ <section ref="./mussagl_manual.html#mussa-c-qt-opengl" title="Mussagl C++/Qt/OpenGL"/>
+ </section>
+ </section>
+
+ <section ref="./mussagl_manual.html#getting-mussagl" title="Getting Mussagl">
+ <section ref="./mussagl_manual.html#license" title="License"/>
+ <section ref="./mussagl_manual.html#platforms" title="Platforms"/>
+ <section ref="./mussagl_manual.html#download" title="Download"/>
+
+ <section ref="./mussagl_manual.html#install" title="Install">
+ <section ref="./mussagl_manual.html#mac-os-x" title="Mac OS X"/>
+ <section ref="./mussagl_manual.html#windows-xp" title="Windows XP"/>
+ <section ref="./mussagl_manual.html#linux" title="Linux"/>
+ <section ref="./mussagl_manual.html#build-from-source" title="Build from Source"/>
+ </section>
+
+ </section>
+
+ <section ref="./mussagl_manual.html#using-mussagl" title="Using Mussagl">
+
+ <section ref="./mussagl_manual.html#launch-mussagl" title="Launch Mussagl"/>
+
+ <section ref="./mussagl_manual.html#create-load-analysis" title="Create/Load Analysis">
+ <section ref="./mussagl_manual.html#create-a-new-analysis" title="Create a new analysis"/>
+ <section ref="./mussagl_manual.html#load-a-mussa-parameter-file" title="Load a mussa parameter file"/>
+ <section ref="./mussagl_manual.html#load-an-analysis" title="Load an analysis"/>
+ </section>
+
+ <section ref="./mussagl_manual.html#main-window" title="Main Window">
+ <section ref="./mussagl_manual.html#overview" title="Overview"/>
+ <section ref="./mussagl_manual.html#dna-sequence-black-bars" title="DNA Sequence (black bars)"/>
+ <section ref="./mussagl_manual.html#annotation" title="Annotation"/>
+ <section ref="./mussagl_manual.html#motif" title="Motif"/>
+ <section ref="./mussagl_manual.html#conservation-tracks" title="Conservation Tracks"/>
+ <section ref="./mussagl_manual.html#motif-toggle" title="Motif Toggle"/>
+ <section ref="./mussagl_manual.html#zoom-factor" title="Zoom Factor"/>
+ <section ref="./mussagl_manual.html#dynamic-threshold" title="Dynamic Threshold"/>
+ <section ref="./mussagl_manual.html#sequence-information-bar" title="Sequence Information Bar"/>
+ <section ref="./mussagl_manual.html#sequence-scroll-bar" title="Sequence Scroll Bar"/>
+ </section>
+
+ <section ref="./mussagl_manual.html#annotations-motifs" title="Annotations / Motifs">
+ <section ref="./mussagl_manual.html#annotations" title="Annotations"/>
+ <section ref="./mussagl_manual.html#motifs" title="Motifs">
+ <section ref="./mussagl_manual.html#load-motifs-from-file" title="Load motifs from File"/>
+ <section ref="./mussagl_manual.html#save-motifs-to-file" title="Save Motifs to File"/>
+ <section ref="./mussagl_manual.html#motif-dialog" title="Motif Dialog"/>
+ </section>
+
+ </section>
+
+ <section ref="./mussagl_manual.html#view-mussa-alignments" title="View Mussa Alignments"/>
+ <section ref="./mussagl_manual.html#saving-to-an-image" title="Saving to an Image"/>
+
+ <section ref="./mussagl_manual.html#detailed-information" title="Detailed Information">
+ <section ref="./mussagl_manual.html#threshold" title="Threshold"/>
+ <section ref="./mussagl_manual.html#window-size" title="Window Size"/>
+ <section ref="./mussagl_manual.html#sequences" title="Sequences"/>
+ </section>
+
+ <section ref="./mussagl_manual.html#mussa-file-formats" title="Mussa File Formats">
+ <section ref="./mussagl_manual.html#parameter-file-format" title="Parameter File Format"/>
+ <section ref="./mussagl_manual.html#annotation-file-format" title="Annotation File Format"/>
+ <section ref="./mussagl_manual.html#motif-file-format" title="Motif File Format"/>
+ <section ref="./mussagl_manual.html#iupac-necleotide-code" title="IUPAC Nucleotide Code"/>
+ </section>
+
+ </section>
+
+
+
+ </DCF>
+</assistantconfig>
\ No newline at end of file