Goalign: toolkit and api for alignment manipulation

Commands

split

This command splits an input alignment according to partitions given as input.

The partitions are defined as in RAxML.

Usage

goalign split -i align.phylip --partition partition.txt


Usage:
  goalign split [flags]

Flags:
  -h, --help                help for split
  -o, --out-prefix string   Prefix of output files
      --partition string    File containing definition of the partitions (default "none")

Global Flags:
  -i, --align string     int  Alignment input file (default "stdin")
      --auto-detect      int  Auto detects input format (overrides -p, -x and -u)
  -u, --clustal          int  Alignment is in clustal? default fasta
      --ignore-identical int  Ignore duplicated sequences that have the same name and same sequences
      --input-strict     int  Strict phylip input format (only used with -p)
  -x, --nexus            int  Alignment is in nexus? default fasta
      --no-block         int  Write Phylip sequences without space separated blocks (only used with -p)
      --one-line         int  Write Phylip sequences on 1 line (only used with -p)
      --output-strict    int  Strict phylip output format (only used with -p)
  -p, --phylip           int  Alignment is in phylip? default fasta

Examples

• Spliting an alignment

input.fa

>s1
AAAACCCCCGG
>2
AAAACCCCCGG
>3
AAAACCCCCGG
>4
AAAACCCCCGG
>5
AAAACCCCCGG

partition.txt

M1,p1=1-4,10-11
M2,p2=5-9

This command:

goalign split -i input.fa --partition partition.txt --out-prefix ./

Should produce:

p1.fa

>s1
AAAAGG
>2
AAAAGG
>3
AAAAGG
>4
AAAAGG
>5
AAAAGG

and p2.fa

>s1
CCCCC
>2
CCCCC
>3
CCCCC
>4
CCCCC
>5
CCCCC