Jalview

Jalview is a multiple sequence alignment editor & viewer written in the Java programming language. It is used widely in a variety of web pages (e.g. the EBI ClustalW server and the Pfam protein domain database) but is available as a general purpose alignment editor.

Additional recommended knowledge

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Use Jalview for:

• Viewing
  • Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
    • Save alignments and associated trees in Jalview XML format.
• Editing
  • Gaps can be inserted/deleted using the mouse or keyboard.
  • Group editing (insertion deletion of gaps in groups of sequences).
  • Removal of gapped columns.
• Analysis
  • Align sequences using Web Services (Clustal, Muscle...)
  • Amino acid conservation analysis similar to that of AMAS.
  • Alignment sorting options (by name, tree order, percent identity, group).
  • UPGMA and NJ trees calculated and drawn based on percent identity distances.
  • Sequence clustering using principal component analysis.
  • Removal of redundant sequences.
  • Smith Waterman pairwise alignment of selected sequences.
• Annotation
  • Use web based secondary structure prediction programs (JNet).
• Annotation
  • User predefined or custom colour schemes to colour alignments or groups.
  • Sequence feature retrieval and display on the alignment.
• Publishing
  • Print your alignment with colours and annotations.
  • Create HTML pages.
  • Output alignment as portable network graphics image (PNG).
  • Output alignment as encapsulated postscript file (EPS).