Sequence Addition

Add sequences to existing sequence files/alignments. Allow adding sequences from multiple sources to multiple destinations. The file formats for the source and destinations can be different, but SEGUL requires matching file names for both to add the sequences. If the destination files are aligned, all the output sequences will be unaligned. We recommend using MAFFT to align the resulting sequence files.

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

Quick start

To add sequences, use the add command with the following options:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir>

For example:

segul sequence add -d source-sequence/ --to-dir destination-sequence/

Specify the input format

The command above will look for any FASTA, NEXUS, or PHYLIP format sequences in the source directory and add them to the destination directory. You can specify the input format using the --input-format option. For example, to add sequences in NEXUS format, use the command below:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir> --input-format nexus

You can specify the destination format using the --to-fmt option. For example, to add sequences in NEXUS format to the destination directory in FASTA format, use the command below:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir> --input-format nexus --to-fmt fasta

Specify the output directory name and format

By default, the output directory will be named Sequence-Addition. You can change the output directory name using the --output or -o option. For example, to name the output directory seq-add, use the command below:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir> --output seq-add

The output format will be in interleaved FASTA format. The other option is in sequential FASTA format. Use the --output-format fasta or -F fasta option to change the output to sequential FASTA format. For example:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir> --output-format fasta

Output only the added sequences

By default, SEGUL will output all sequences in the destination directory. If the destination directory format differs from the output format, all the output will be changed to the selected output format. If you only want to output files with the added sequences, use the --added-only flag. For example:

segul sequence add -d <source-sequence-dir> --to-dir <destination-sequence-dir> --added-only

All options

Option	Description
-d, --dir	Directory with the sequences to add
-i, --input	Sequence files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
--to-dir	Directory with the files to add sequences to
--to-input	Files to add sequences to. Allows wildcards
--to-fmt	Format of the files to add to: auto (default), fasta, nexus, or phylip
--to-file	Add all sequences to a single file instead
--added-only	Only write files that received new sequences
--include-filename	Add the source file name to sequence IDs. Only with --to-file
-F, --output-format	Output format: fasta-int (default) or fasta
-o, --output	Output directory. Default: Sequence-Addition
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log