Contents

• Introduction
  • Requirements
  • Download
  • Installation
  • Found a bug?
  • Citation
  • Copyright and licence
  • Acknowledgements
• Manual
  • Basic usage
  • Adding HTML
  • Consensus sequences
  • Colouring modes
  • Colours
  • Layout and filtering
  • Data formats
  • Linking identifiers to external resources
  • Memory usage
• Input formats
  • NCBI BLAST family
  • WashU-BLAST family
  • Uni. Virginia FASTA family
  • CLUSTAL/aln
  • HSSP
  • MAF
  • FASTA
  • MSF
  • PIR
  • plain
  • Unsupported
• Output formats
  • plain
  • FASTA
  • CLUSTAL/aln
  • PIR
  • MSF
  • RDB
• BLAST HSP processing rules
  • Output modes
  • Algorithm for tiling HSPs
  • More details about each BLAST program
• Frequently asked questions
  • Can MView extract BLAST (or other) output into a FASTA/PIR/MSF/CLUSTAL file?
  • Can MView extract or view the separate BLAST alignment or HSPs?
  • Does MView work with nucleotide sequences?
  • Can MView use CLUSTAL colours?
  • Can MView process data from a Web page?
  • Can I switch off HTML markup?
  • How can I print?
  • Can I edit the alignment?
  • What do the percent identities mean?
  • Why are some symbols lowercased?
  • Why is the query sequence incomplete?
  • How are overlapping BLAST HSPs processed?
• Licence