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).
Usage:
goalign concat [flags] [alignment files]
Flags:
-o, --output string Alignment output file (default "stdout")
-l, --log string Log output file (coordinates of all input alignments
in the concatenated alignment) (default "none")
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)
- 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