append.md

Goalign: toolkit and api for alignment manipulation

Commands

append

Append alignments to an input alignment by inserting new sequences.

This commands adds the sequences of a set of alignments to a reference alignement specified by -i.

If sequences do not have the same length than the reference alignment, then returns an error.

If format is phylip, it may contain several alignments in one file and then we can append all of them at once:

goalign append -i refalign.phy aligns.phy

If format is Fasta, several alignments may be given in the form:

goalign append -i align.fasta others*.fasta

Usage

General command

Usage:
  goalign append [flags]

Flags:
  -h, --help            help for append
  -o, --output string   Alignment output 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
      --ignore-identical  int Ignore duplicated sequences that have the same name and same sequences
      --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

• Append 3 alignments

cat > input.1 <<EOF
>s1
ACGACGACGACC
>2
ATCTT-TTTTTC
>3
ATCTT-TTTTTT
EOF

cat > input.2 <<EOF
>s4
ACGACGACGACC
>5
ATCTT-TTTTTC
>6
ATCTT-TTTTTT
EOF

cat > input.3 <<EOF
>s7
ACGACGACGACC
>8
ATCTT-TTTTTC
>9
ATCTT-TTTTTT
EOF

goalign append -i input.1 input.2 input.3 

>s1
ACGACGACGACC
>2
ATCTT-TTTTTC
>3
ATCTT-TTTTTT
>s4
ACGACGACGACC
>5
ATCTT-TTTTTC
>6
ATCTT-TTTTTT
>s7
ACGACGACGACC
>8
ATCTT-TTTTTC
>9
ATCTT-TTTTTT