dedup.md

Goalign: toolkit and api for alignment manipulation

Commands

dedup

This command deduplicates sequences. To do so it removes identical sequences.

If -l is specified, then identical sequences are printed in the given file with the following format:

seq1,seq2
seq3,seq4

This means that seq1 is identical to seq2 and seq3 is identical to seq4.

if --n-as-gap is specified: X/N (depending on alphabet) are considered identical to GAPS for identifying identical sequences. Only the first sequence appears in the output alignment.

Usage

Usage:
  goalign dedup [flags]

Flags:
  -h, --help            help for dedup
  -l, --log string      Deduplicated output log file (default "none")
      --n-as-gap        Considers N/X identical to GAPS for identifying identical sequences
      --name            Deduplicate by name instead of sequence event if sequences are different (only the first appears in the output file)
  -o, --output string   Deduplicated output alignment file (default "stdout")
      --unaligned       Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored)

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
      --auto-detect     Auto detects input format (overrides -p, -x and -u)
  -u, --clustal         Alignment is in clustal? default fasta
      --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

cat > input.phy <<EOF
   6   6
3  GGGGGG
1  AAAAAA
2  CCCCCC
4  GGGGGG
4  GGGGGG
EOF

goalign dedup -i input.phy --phylip

should output:

   3   6
3  GGGGGG
1  AAAAAA
2  CCCCCC