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Goalign: toolkit and api for alignment manipulation

Commands

draw

This command draws alignments with basic functionalities. So far, output format is html, using BioJS library, and PNG displaying one sequence per line and one pixel per character.

If the input file contains several alignments, it will write several output files.

Usage

  • general command:
Usage:
  goalign draw [command]

Available Commands:
  biojs       Draw alignments in html file using msaviewer from biojs
  png         Draw alignments in a png file

Flags:
  -o, --output string   Alignment draw output file (default "stdout")

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
      --auto-detect     Auto detects input format (overrides -p and -x)
      --input-strict    Strict phylip input format (only used with -p)
  -x, --nexus           Alignment is in nexus? default fasta
      --output-strict   Strict phylip output format (only used with -p)
  -p, --phylip          Alignment is in phylip? default fasta
  • biojs subcommand
Usage:
  goalign draw biojs [flags]

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
      --auto-detect     Auto detects input format (overrides -p and -x)
      --input-strict    Strict phylip input format (only used with -p)
  -x, --nexus           Alignment is in nexus? default fasta
  -o, --output string   Alignment draw output file (default "stdout")
  -p, --phylip          Alignment is in phylip? default fasta
  • png subcommand
Usage:
  goalign draw png [flags]

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
      --auto-detect     Auto detects input format (overrides -p and -x)
      --input-strict    Strict phylip input format (only used with -p)
  -x, --nexus           Alignment is in nexus? default fasta
  -o, --output string   Alignment draw output file (default "stdout")
  -p, --phylip          Alignment is in phylip? default fasta

Examples

  • Generating a random alignment and displaying it in html
goalign random -l 10 --seed 10 | goalign draw biojs -o al.html

Should give the following alignment: HTML Display

  • Generating a random nucleotide alignment and displaying it in png
goalign random -l 10 --seed 10 | goalign draw png -o al.png

Should give the following image: HTML Display