<?xml version="1.0" encoding="ISO-8859-1" ?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+
+ This file is part of Jalview.
+
+ Jalview is free software: you can redistribute it and/or
+ modify it under the terms of the GNU General Public License
+ as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ Jalview is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty
+ of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
<toc version="1.0">
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
- <tocitem text="Release History" target="release"/>
- <tocitem text="Sequence Retrieval" target="seqfetch"/>
- <tocitem text="VAMSAS Interoperation" target="vamsas"/>
+ <tocitem text="Protein Disorder Prediction" target="disorder"/>
+ <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ <tocitem text="HTML annotation report" target="io.seqreport"/>
+ <tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
+ <tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
+ <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
+ <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
+ <tocitem text="DNA or Protein PCA calculation" target="pca"/>
+ <tocitem text="Normalised sequence logo display" target="calcs.consensus"/>
</tocitem>
<tocitem text="Editing Alignments" target ="edit"/>
<tocitem text="Cursor Mode" target="cursor"/>
<tocitem text="Multiple Views" target="multipleviews"/>
<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
<tocitem text="Fetching Sequences" target="seqfetch"/>
+ <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ </tocitem>
<tocitem text="Sequence Features" target="seqfeatures" expand="false">
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
<tocitem text="Sequence Features File" target="features.fileformat"/>
<tocitem text="Editing Sequence Features" target="seqfeatedit"/>
<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
<tocitem text="DAS Feature Settings" target="das.settings"/>
+ <tocitem text="HTML annotation report" target="io.seqreport"/>
</tocitem>
<tocitem text="Web Services" target="webservice" expand="false">
- <tocitem text="Sequence Alignment" target="msaservice" expand="false">
- <tocitem text="Clustal Alignment" target="clustal"/>
- <tocitem text="Muscle Alignment" target="muscle"/>
- <tocitem text="MAFFT Alignment" target="mafft"/>
+ <tocitem text="JABAWS" target="jabaws"/>
+ <tocitem text="Web Service Preferences" target="wsprefs"/>
+ <tocitem text="Web Service Parameters" target="wsparams"/>
+ <tocitem text="Sequence Alignment" target="msaservice" expand="false">
<tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <tocitem text="Protein Disorder Prediction" target="disorder"/>
+ <tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
<tocitem text="Sequence Retrieval" target="seqfetch"/>
+ <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
</tocitem>
<tocitem text="Colour Schemes" target="colours" expand="false">
<tocitem text="Turn propensity" target="colours.turn"/>
<tocitem text="Buried index" target="colours.buried"/>
<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+ <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
<tocitem text="Blosum62" target="colours.blosum"/>
<tocitem text="by Percentage Identity" target="colours.pid"/>
<tocitem text="User Defined" target="colours.user"/>
<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
<tocitem text="By conservation" target="colours.conservation"/>
+ <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
<tocitem text="By Annotation" target="colours.annotation"/>
+ <tocitem text="By RNA Helices" target="colours.rnahelices"/>
</tocitem>
<tocitem text="Calculations" target="calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv"/>
+ <tocitem text="Conservation" target="calcs.alconserv"/>
<tocitem text="Quality" target="calcs.alquality"/>
<tocitem text="Consensus" target="calcs.consensus"/>
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<tocitem text="Annotations File Format" target="annotations.fileformat"/>
</tocitem>
<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
<tocitem text="Jmol Viewer" target="pdbjmol"/>
<tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
</tocitem>
+ <tocitem text="Viewing RNA structures" target="varna" expand="false"> </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
</tocitem>
<tocitem text="Privacy" target="privacy"/>
</tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
<tocitem text="Amino Acid Table" target="aminoAcids"/>
<tocitem text="Amino Acid Properties" target="aaProperties"/>
<tocitem text="The Genetic Code" target="geneticCode"/>
+ <tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+
</tocitem>
</toc>