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Goalign: toolkit and api for alignment manipulation

Commands

reformat

This command reformats an input alignment (fasta by default or phylip with -p) in different formats depending on the sub-command:

  1. goalign reformat fasta: reformats input alignment in fasta;
  2. goalign reformat nexus: reformats input alignment in nexus;
  3. goalign reformat phylip: reformats input alignment in phylip;
  4. goalign reformat tnt: reformats input alignment in TNT input format.

Usage

  • general command:
Usage:
  goalign reformat [command]

Available Commands:
  clustal     Reformats an input alignment into Clustal
  fasta       Reformats an input alignment into Fasta
  nexus       Reformats an input alignment into nexus
  phylip      Reformats an input alignment into Phylip
  paml        Reformats an input alignment into input data for PAML
  tnt         Reformats an input alignment into input data for TNT

Flags:
  --clean-names     Replaces special characters (tabs, spaces, newick characters) with '-'
                    from input sequence names before writing output alignment
  -o, --output string   Reformated alignment output file (default "stdout")
  -s, --strict          If it is strict phylip format

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

If --clean-names option is given, special characters in sequence names (that may conflict with newick format after tree inference) are replaced by -.

Examples

  • Generating a random fasta alignment with 5 sequences and 5 nucleotides and reformating it in phylip:
goalign random -n 5 -l 5 --seed 10 | goalign reformat phylip

Should give the following alignment:

  5   5
Seq0000  GATTA
Seq0001  ATTTG
Seq0002  CCGTA
Seq0003  GGCCA
Seq0004  GAATC
  • Generating a random fasta alignment with 5 sequences and 5 nucleotides and reformating it in nexus:
goalign random -n 5 -l 5 --seed 10 | goalign reformat nexus

Should give the following alignment:

#NEXUS
begin data;
dimensions ntax=5 nchar=5;
format datatype=nucleotide;
matrix
Seq0000 GATTA
Seq0001 ATTTG
Seq0002 CCGTA
Seq0003 GGCCA
Seq0004 GAATC
;
end;