fu-msa

Note

Preliminary version

Interactive multiple sequence alignment viewer from the Command Line.

Multiple sequence aligner

Usage:
    full [options] <MSAFILE>
  
  Keys:
    Scroll Horizontally     Left and Right arrow
      By 10 bases           L, K
      By 100 bases          ShiftL, ShiftK
      To the beginning      1
      To middle parts       2..9
      To the end            0

    Scroll Vertically       A, Up Arrow/ Z, Down Arrow
      Jump to top           ShiftA, PageUp
      Jump to bottom        ShiftZ, PageDown

    Rotate color scheme     Tab
    Refresh screen          F5
    Resize seq labels       -,+
    Search                  / (seqname, ":INT", "#SEQ")
    Quit                    Q, CtrlC

  Options:
    -m, --mouse               Enable mouse
    -n, --norefresh           Disable autorefresh
    -j, --jumpsize INT        Jump size (big jump is 10X) [default: 10]

  Visualization settings:
    -i, --seqindex INT        Start visualization at this sequence [default: 0]
    -p, --seqpos INT          Start visualization at this nucleotide [default: 0]
    -w, --label-width INT     Sequence label width [default: 20]
    -s, --setting-string STR  Settings string (overrrides all other settings) is in the
                              format Seq:{seqindex}:{seqpos}:{labelwidth} and is the 
                              return value of the program when it is closed.

    More documentation online at https://telatin.github.io/seqfu2/

Keyboard

Horizontal scrolling

  • :arrow_left:, :arrow_up: : scroll by one nucleotide
  • K, L: scroll left and right respectively, by 10 nucleotides
  • Shift + K, Shift + L: scroll left and right respectively, by 100 nucleotides
  • End: Move to sequence end
  • Home: Move to the beginning of the sequence
  • 1: Move to the first base
  • 2..9: Move to 20% .. 90% of the sequence
  • 0: Move to the last base

Vertical scrolling

  • A, Z and :arrow_up:, :arrow_down: : Move up and down by one sequence
  • Shift + A, Shift + Z: Move to top and move to bottom

  • / Trigger search, then:

    • Type the query
    • Hit Enter to submit or Esc to abort

  • The query can be:

    • part of a sequence name
    • : followed by a sequence index (eg: :0 to go to the first sequence)
    • # followed by a sequence (eg: #ATTAC to jump to the position of the first occurrence of ATTAC)

Visualization

  • Space: toggle consensus sequence from "Consensus" (show bases identical across all the sequences) to "Majority" (show bases shared by 50% of the sequences or more)
  • Tab: toggle color scheme
  • -,+: Decrease and increase by one the sequence label width
  • F5, R: refresh
  • F6: toggle autorefresh on/off
  • H: toggle help screen (only major keys are reported)

Mouse

  • M: toggle mouse on/off
  • When mouse is on:
    • Click in a nucleotide to set that position as first (scroll right)
    • Click to the sequence name area (left) to scroll left

Resuming session

When pressing quit (Q) the program will print a configuration string like: Seq:0:6:20 that can be used to resume the session at the same position with:

fu-msa {input_file} --setting-string Seq:0:6:20

The settings string is in the format Seq:{seqindex}:{seqpos}:{labelwidth}

Colors

  • DNA: A (red), C (cyan), G (green), T (yellow)
  • Protein: "Lesk" scheme:
    • Hydrophobic, green
    • Small non polar, yellow (should be orange)
    • Polar, magenta
    • Negative charge, red
    • Positive charge, cyan (should be blue)

Screenshot

Screenshot of