Concatenating alignments

segul provides an easy way to concat multiple alignments and generate the partition setting at the same time.

segul concat <input-argument> [input-path] --input-format [sequence-format]

For example, we will concat all the alignments in this folder:

alignments/
├── locus_1.nexus
├── locus_2.nexus
└── locus_3.nexus

We can do it in two ways. First, using --dir argument to input alignment files:

segul concat --dir alignments/ --input-format nexus

Second, we can use the --input argument to input the alignment files. We will rely on wildcard and the OS to find all the alignment files. We do not need to specify the input format for .nexus file extension:

segul concat --input alignments/*.nexus

segul will generate two files saved in SEGUL-concat directory, consisting of the concatenated alignments and the partition settings:

SEGUL-concat/
├── SEGUL-Concat.nex
└── SEGUL-Concat_partition.nex

To specify the name of the output directory, use the --output or -o option. Below, we will name our output directory aln-concat.

segul concat --input alignments/*.nexus --output aln-concat

To specify the prefix of the file names use the --prefix option. Below, our output filenames will start with concat:

segul concat --input alignments/*.nexus --output aln-concat --prefix concat

The resulting output directory will contain files as below:

aln-concat/
├── concat.nex
└── concat_partition.nex

By default, the partition format is in nexus:

#nexus
begin sets;
charset 'locus-1' = 1-666;
charset 'locus-2' = 667-1473;
charset 'locus-3' = 1474-2000;
end;

You can specify the partition format using --part or -p option.

For example, to use raxml format:

segul concat --input alignments/*.nexus --output concat --prefix concat --part raxml

The resulting partioned will be formatted in raxml style:

DNA, locus_1 = 1-666
DNA, locus_2 = 667-1473
DNA, locus_3 = 1474-2000

If the input is amino acid sequence, the partion will not contain the datatype:

The resulting partioned will be formatted in raxml style:

locus_1 = 1-666
locus_2 = 667-1473
locus_3 = 1474-2000

You can also use charset format. In this format, the partition will be written at the end of the sequence and only available for the nexus output. This format is usually required for phylogenetic programs, such PAUP and BEAST. To use charset format:

segul concat --input alignments/*.nexus --output concat --prefix concat --part charset

You can also write the partition to a codon model format by using the flag --codon. You may not need this option for genomic datasets. We reserve this function for Sanger datasets.