Contents

Jalview Documentation
   What's new
      Latest Release Notes
      PaSiMap Sequence Similarity Plots
      Secondary Structure Trees and PCAs
      Secondary Structure Consensus
   Editing Alignments
   Cursor Mode
   Key Strokes
   Input / Output
      BioJSON v1.0
   Making Figures
      BioJS MSA Viewer
   Hidden Regions
   Multiple Views
   Split Frame View
   Viewing Trees
   Fetching Sequences
   Select Columns by Annotation
   Nucleic Acid Support
      Annotating from VCF
      Viewing RNA structure
      RNA Structure Consensus
      RNA Helices coloring
   Sequence Features
      Sequence Feature Settings
      Sequence Features File
      Feature Colourschemes
      User Defined Sequence Features
      Editing Sequence Features
      HTML Feature Attributes report
      HTML annotation report
   Web Services
      JABAWS
      Web Service Preferences
      Web Service Parameters
      Sequence Alignment
         Multiple Alignment Subjobs
      Secondary Structure Prediction
      RNAalifold RNA Secondary Structure Prediction
      Protein Disorder Prediction
      Alignment Conservation Analysis
      Multi-Harmony Alignment Analysis
      Sequence Retrieval
      Database Reference Retrieval
   Colour Schemes
      Background Dependent Text Colour
      ClustalX
      Zappo
      Taylor
      gecos Flower
      gecos Blossom
      gecos Sunset
      gecos Ocean
      Hydrophobicity
      Helix propensity
      Strand propensity
      Turn propensity
      Buried index
      Nucleotide colours
      Nucleotide Ambiguity colours
      Purine/Pyrimidine colours
      Blosum62
      by Percentage Identity
      User Defined
      Above Percentage Identity
      By conservation
      T-COFFEE Scores
      By Annotation
      By RNA Helices
   Calculations
      Sorting alignments
      Trees, PCA and PaSiMap
         Calculating trees
         Principal Component Analysis
         PaSiMap Analysis
      Tree/PCA Input Data
      Pairwise Alignments
      Remove Redundancy
      Reference Sequences
   Sequence Annotations
      Annotation from Structure
   Alignment Annotations
      Conservation
      Quality
      Consensus
      RNA Structure Consensus
      Annotations File Format
      Select Columns by Annotation
   3D Structure Data
      PDB Sequence Fetcher
      PDB & 3D-Beacons Structure Chooser
      Jmol Viewer
      Chimera/X Viewer
      Pymol Viewer
   Viewing RNA structures
   Opening URLs from Jalview
      Configuring URL Links
   Window Menus
      Desktop Window
      Alignment Window
         File Menu
         Edit Menu
         Select Menu
         View Menu
         Annotations Menu
         Format Menu
         Colour Menu
         Calculate Menu
         Web Service Menu
         Annotation Panel Menu
         Popup Menu
   Preferences
   The Java Console, Logging and Reporting Bugs
   Scripting with Groovy
      Groovy Features Counter example
   Command Line
      Command Line: introduction and reference
      Command Line: basic usage
      Command Line: advanced usage
      Command Line: argument files
      Command Line: reference
      Command Line: old command line arguments
   Memory Settings
   Jalview Launch Files
   Privacy
Useful information
   Amino Acid Table
   Amino Acid Properties
   The Genetic Code
   Sequence Substitution Matrices