random.md

Goalign: toolkit and api for alignment manipulation

Commands

random

This command generate a random alignment with uniform distribution of nucleotides or amino acids. It is intended for testing purpose, as no evolutionary information is taken into account.

Usage

Usage:
  goalign random [flags]

Flags:
  -a, --amino-acids        Aminoacid sequences (otherwise, nucleotides)
  -l, --length int         Length of sequences to generate (default 100)
  -n, --nb-seqs int        Number of sequences to generate (default 10)
  -o, --out-align string   Random alignment output file (default "stdout")
      --seed int           Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

Examples

• Generating a random alignment with 100 sequences and 1000 nucleotides:

goalign random -n 100 -l 1000 --seed 10 | goalign stats

Should give the following statistics:

length	1000
nseqs	100
avgalleles	4.0000
char	nb	freq
A	24899	0.248990
C	25032	0.250320
G	24888	0.248880
T	25181	0.251810