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Goalign: toolkit and api for alignment manipulation

Commands

sort

This command sort an input alignment by sequence names.

Usage

Usage:
  goalign sort [flags]

Flags:
  -o, --output string   Sorted alignment output file (default "stdout")

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
  --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

Examples

  • Sorting a random alignment
goalign random --seed 10 -l 10 -n 5 | goalign shuffle seqs | goalign sort

It should give the following alignment:

>Seq0000
GATTAATTTG
>Seq0001
CCGTAGGCCA
>Seq0002
GAATCTGAAG
>Seq0003
ATCGAACACT
>Seq0004
TTAAGTTTTC