Sequence Addition (Beta)
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.
This feature is still in beta. Please report any issues you encounter. For more information, see the Try Beta Features section.
Quick Start
To add sequences, use the add command with the following options:
segul sequence add -d <source-sequence-dir> --destination-dir <destination-sequence-dir>
For example:
segul sequence add -d source-sequence/ --destination-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> --destination-dir <destination-sequence-dir> --input-format nexus
You can specify the destination format using the --destination-format 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> --destination-dir <destination-sequence-dir> --input-format nexus --destination-format 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> --destination-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> --destination-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> --destination-dir <destination-sequence-dir> --added-only