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Goalign: toolkit and api for alignment manipulation

Commands

divide

This command divides an input alignment file (phylip format) containing several alignments, in multiple files containing one alignment. If alignment is in Fasta, will create only one file. Option -o indicates prefix of output files.

Usage

Usage:
  goalign divide [flags]

Flags:
  -f, --out-fasta       Output files in fasta format (default, same as input)
  -o, --output string   Divided alignment output files prefix (default "prefix")

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

Examples

  • Generating a random tree with 5 tips (Gotree), simulating 3 alignments from this tree (seq-gen), and writing them in 3 independ fasta files:
gotree generate yuletree -l 5 --seed 1 -o true_tree.nw
seq-gen -op -mGTR -l500 -z 2 -n 3 true_tree.nw | goalign divide -p -f -o align

There should be three files in the current directory:

  • align_000.fa
  • align_001.fa
  • align_002.fa