orf.md

Goalign: toolkit and api for alignment manipulation

Commands

orf

Find the longest orf in all given sequences in forward strand.

If input sequences are not nucleotidic, then returns an error.

If input sequences are aligned (contain '-'), then they are unaligned first.

Output is in fasta format (format options such as -p and -x are ignored).

Usage

Usage:
  goalign orf [flags]

Flags:
  -h, --help            help for orf
  -o, --output string   ORF Output Fasta File (default "stdout")

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
      --no-block        Write Phylip sequences without space separated blocks (only used with -p)
      --one-line        Write Phylip sequences on 1 line (only used with -p)
      --output-strict   Strict phylip output format (only used with -p)
  -p, --phylip          Alignment is in phylip? default fasta

Examples