Goalign: toolkit and api for alignment manipulation

Commands

concat

This command concatenates several alignments in one global alignment. Input alignments may be in phylip or fasta format. If input format is phylip, the file may contain several alignments to concatenate : goalign concat -i several.phy. If format is Fasta, all fasta files must be given independently with goalign concat -i first.fa [second.fa, third.fa, ...] or goalign -i none [first.fa, second.Fa, third.fa, ...]. The order of sequences in alignments may be different, concat command will match sequences based on their name.

If -l is given, the coordinates of all the input alignments in the concatenated alignment are written in the log file (tab separated values : start (0-based inclusive), end (0-based exclusive), input file name).

If --out-partitionis provided, a partition file is written at the specified location, with each partition matching its source alignment. The default model is GTR for nucleotide alignments and LG for aminoacid alignments.

Usage

Usage:
  goalign concat [flags] [alignment files]

Flags:
  -h, --help                   help for concat
  -l, --log string             Log output file (coordinates of all input alignments 
                               in the concatenated alignment) (default "none")
      --out-partition string   File containing output partitions (default "none")
  -o, --output string          Alignment output file (default "stdout")

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 tree with 5 tips (Gotree), simulating 3 alignments from this tree (seq-gen), shuffle sequence order, and concatenating them:

gotree generate yuletree -l 5 --seed 1 -o true_tree.nw
seq-gen -op -mGTR -l500 -z 2 -n 3 true_tree.nw | goalign shuffle seqs -p > alignment.phy
goalign concat -i alignment.phy -p | goalign stats -p

It should give the following statistics:

length	1500
nseqs	5
avgalleles	1.3220
char	nb	freq
A	1894	0.252533
C	1898	0.253067
G	1788	0.238400
T	1920	0.256000