Contents

• Manual
  • Basic usage
    • Getting started
    • The ruler line
    • Command line options
  • Layout and filtering
    • Pagination
    • Column ranges
    • Changing the reference sequence
    • Sorting by percent coverage or percent identity
    • Filtering rows
    • Labels, annotations and sequences
  • Adding HTML
    • Basic HTML
    • Controlling the amount of HTML
    • Using an external CSS style sheet
  • Consensus sequences
    • Clustal conservation line
    • Consensus lines
    • Changing consensus thresholds
    • Consensus pattern definitions
    • Changing consensus patterns
    • Showing conserved residues or conserved classes
  • Colouring modes
    • Alignment colouring
    • Conserved residue colouring
    • Finding and colouring motifs
    • Combining alignment and motif colouring
    • Comment row colouring
    • Consensus pattern colouring
  • Colours
    • Colourmaps
    • Creating new colourmaps
  • Coverage and identity
    • Percent coverage
    • Percent identity
  • Data formats
    • Input formats
    • Output formats
  • Linking identifiers to external resources
  • Memory usage and speed
• Input formats
  • NCBI BLAST family
    • BLAST+
    • BLAST series 2.2
    • BLAST series 2.0
    • BLAST series 1.4
  • WashU-BLAST family
    • WU-BLAST series 2.0
  • Uni. Virginia FASTA family
    • FASTA series 36
    • FASTA series 35
    • FASTA series 34
    • FASTA series 3.0 - 3.4
    • FASTA series 2
    • FASTA series 1
  • CLUSTAL/aln
  • HSSP/Maxhom
  • MAF
  • FASTA
  • MSF
  • PIR
  • plain
  • Unsupported
• Output formats
  • plain
  • mview
  • FASTA
  • CLUSTAL/aln
  • PIR
  • MSF
  • RDB
• BLAST HSP processing rules
  • Output modes
  • Algorithm for tiling HSPs
  • More details about each BLAST program
    • NCBI BLAST series 1 and WU-BLAST series 2
      • BLASTP
      • BLASTN
      • BLASTX
      • TBLASTN
      • TBLASTX
      • Column headings
      • Key
      • Differences between NCBI BLAST 1 and NCBI BLAST 2
    • NCBI BLAST series 2 and NCBI BLAST+
      • BLASTP
      • BLASTN
      • BLASTX
      • TBLASTN
      • TBLASTX
      • PSI-BLAST
      • Column headings
      • Key
• Frequently asked questions
  • Can MView extract BLAST (or other) output into a FASTA/PIR/MSF/CLUSTAL file?
  • 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?
  • Can MView extract or view the alternative BLAST alignments or HSPs?
  • Why are some sequence symbols lowercased?
  • Can I extract BLAST hits complete with insertions?
  • Why is the query sequence incomplete?
  • How are overlapping BLAST HSPs processed?
• Licence