Welcome to the SEDA manual!

SEDA

• Introduction
• Installation and configuration
  • Docker
    • Linux
    • Windows
    • Mac OS
  • Dependencies
    • BLAST
    • Clustal Omega
    • bedtools
    • EMBOSS
    • Splign/Compart
    • ProSplign/ProCompart
    • SAPP
• Graphical user interface
  • The Input area
  • The Output area
• Operations
  • Alignment-related
    • Clustal Omega Alignment
    • Concatenate sequences
    • Consensus sequence
    • Undo alignment
  • BLAST
    • Blast
    • Blast: two-way ortholog identification
  • Filtering
    • Base presence filtering
    • Filtering
    • Pattern filtering
    • Remove isoforms
    • Remove redundant sequences
  • Gene Annotation
    • Augustus (SAPP)
    • getorf (EMBOSS)
    • ProSplign/ProCompart Pipeline
    • Splign/Compart Pipeline
  • General
    • Compare
    • Grow sequences
    • Merge
    • Regular expression split
    • Split
    • Translate
  • Reformatting
    • Disambiguate sequence names
    • NCBI rename
    • Reallocate reference sequences
    • Reformat file
    • Rename header
    • Sort
• Advanced usage
  • Pattern configuration
  • Regular expressions
    • Special characters
    • Quantifiers
    • Boundary matchers
• Developers
  • Basic concepts
    • The DatatypeFactory (Abstract Factory pattern)
  • Operations and plugins
    • The SedaContext
  • Architecture
    • How to implement a module
  • Running external software
  • Building the installers
    • Adding a new module to the installers
  • Developing with Eclipse
  • Quick-start module
    • 1. Setting up the module
    • 2. Implementing SequenceTransformation
    • 3. Implementing TransformationProvider
    • 4. Implementing the GUI editor component
    • 5. Implementing SedaGuiPlugin
    • 6. Implementing SedaPluginFactory