stats.md

Goalign: toolkit and api for alignment manipulation

Commands

stats

This command prints different characteristics of the alignment. Without any subcommand, it prints the following information:

1. Length of alignment;
2. Number of sequences;
3. Average number of alleles per site;
4. Number of variables sites (does ot take into account gaps or special characters);
5. Character frequencies.
6. Aphabet

Different sub-commands:

• goalign stats alleles: Prints the average number of alleles per site of the alignment;
• goalign stats alphabet: Prints the alphabet of the alignemnts (aminoacids, nucleotides, unknown);
• goalign stats char: Prints the character frequencies;
• goalign stats length: Prints alignment length;
• goalign stats maxchar: Prints max occurence char for each alignment site
• goalign stats nalign: Prints the number of alignments in the input file (Phylip);
• goalign stats nseq: Prints the number of sequences in the input alignment;
• goalign stats taxa: Lists taxa in the input alignment.

Usage

• General command:

Usage:
goalign stats [flags]
goalign stats [command]
  
Available Commands:
	alleles
	alphabet
	char
	length
	nalign
	nseq
	taxa
			  
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)

Examples

• Generating a random (uniform) alignment and printing stats:

goalign random -l 20 --seed 10| goalign stats

Should give:

length 20
nseqs 10
avgalleles 3.7500
char nb freq
A 54 0.270000
C 34 0.170000
G 49 0.245000
T 63 0.315000
alphabet	nucleotides