Welcome to the SEDA manual!

SEDA

• Introduction
• Installation and configuration
  • SEDA Installation
  • Docker installation
  • Dependencies
  • Increasing RAM memory
• Graphical user interface
  • The Input area
  • The Process area
  • The Output area
• Command-line interface
  • Input options
  • Output options
  • Command configuration files
  • Configuration options
• Operations
  • Alignment-related
  • BLAST
  • Filtering
  • Gene Annotation
  • General
  • Protein Annotation
  • Reformatting
• Protocols
  • Preparing datasets for large scale phylogenetic analyses
  • Obtaining protein family members
  • Protocol for a phylogenomics study
• Pipelines
• Advanced usage
  • Pattern configuration
  • Regular expressions
• Developers
  • Basic concepts
  • Operations and plugins
  • Architecture
  • Running external software
  • Building the installers
  • Developing with Eclipse
  • Quick-start module
• FAQ
  • Is it possible to increase the amount of memory that SEDA uses?
  • Why does an error saying “Java heap space” appears when processing a dataset?