Unalign Alignments

Unalign alignments to produce unaligned sequence files.

Under the hood, SEGUL will read the alignment files and remove all gap characters to produce unaligned sequences. SEGUL can do it for thousands of files in a single command.

Note

This feature is available in SEGUL v0.23.0 and later versions. To check your SEGUL version, run in your terminal:

segul --version
# Compatible version example:
# segul 0.23.0

Check the Installation Guide to update SEGUL to the latest version.

Assume we have an alignment file in FASTA format as follows:

>seq1
ATGCAT--A
>seq2
ATGCATA--
>seq3
ATGCAA-A-
>seq4
ATGCATA--

To unalign the sequences, use the following command:

segul align unalign --dir alignments/

The output will be as follows, with all gap characters removed:

>seq1
ATGCATA
>seq2
ATGCATA
>seq3
ATGCAAA
>seq4
ATGCATA

Detailed usage

Unaligning alignments (DNA)

To unalign alignments, use the align unalign command with the following options. It will automatically detect the input format.

segul align unalign --dir <alignment-dir>

Unaligning alignments (Amino Acid)

To unalign amino acid alignments, use the --datatype aa option as follows:

segul align unalign --dir <alignment-dir> --datatype aa

Specifying output directory

By default, the output directory will be named Align-Unalign in the current working directory. You can change the output directory name using the --output or -o option. For example, to name the output directory unalign-output, use the command below:

segul align unalign --dir <alignment-dir> --output unalign-output

Note

Due to the nature of unaligning, the output format will always be in FASTA format. Use --output-format fasta for sequential FASTA instead of the default interleaved FASTA.

More ways to specify input files

You can also specify input files using the --input or -i option. This option allows you to provide a single alignment file or multiple alignment files using wildcards. For example:

segul align unalign --input alignments/*.fasta

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: fasta-int (default) or fasta
-o, --output	Output directory. Default: Align-Unalign
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log