Goalign: toolkit and api for alignment manipulation

Commands

consensus

This command generates a basic "majority consensus" sequence, i.e. a single sequence whose sites correspond to the majority characters at each positions.

If '-' is the most abundant character, then '-' will be in the consensus, except if --ignore-gaps is specified. If --ignore-gapsis specified, then the majority is computed on non gaps characters, except if the column is only made of gaps. If 'N' is the most abundant character, then 'N' will be in the consensus, except if --ignore-n is specified. If --ignore-nis specified, then the majority is computed on non N/n characters (X/x for proteins), except if the column is only made of N/n (X/x).

Usage

Usage:
  goalign consensus [flags]

Flags:
  --exclude-gaps        Exclude gaps in the majority computation
  -h, --help            help for consensus
  -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
      --ignore-gaps           Ignore gaps (except if only gaps on the column)
      --ignore-n              Ignore Ns  (except if only N on the column)
      --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

• Consensus of 3 sequences:

Input alignment al.fa:

>s1
ACGACGACGACC
>2
ATCTT-TTTTTC
>3
ATCTT-TTTTTT

$ goalign consensus -i al.fa

>consensus
ATCTT-TTTTTC