Alignment Concatenation

SEGUL CLI provides an easy way to concatenate multiple alignments and generate the partition setting simultaneously.

segul align 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, use --dir argument to input alignment files:

segul align concat --dir alignments/

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.

segul align concat --input alignments/*.nexus

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

Align-Concat/
├── Align-Concat.nex
└── Align-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 align 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 align concat --input alignments/*.nexus --output aln-concat --prefix concat

The resulting output directory will contain the files 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 the --partition-format or -p option.

For example, to use RaXML format:

segul align concat --input alignments/*.nexus --output concat --prefix concat --partition-format raxml

The resulting partition 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 sequences, the partition will not contain the datatype:

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 as PAUP and BEAST. To use charset format:

segul align concat --input alignments/*.nexus --output concat --prefix concat --partition-format charset

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

To sort the sequences in the output by their IDs, add the --sort flag.

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
-F, --output-format	Output format: nexus (default), phylip, fasta, nexus-int, phylip-int, or fasta-int
-p, --partition-format	Partition format: nexus (default), charset, or raxml
--codon	Write the partition as a codon model
--sort	Sort sequences by ID
-o, --output	Output directory. Default: Align-Concat
--prefix	Prefix of the output files. Default: Align-Concat
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log