Alignment Concatenation

Desktop

ABCDE

Phone

ABCDE

• AAlignments tab
• BTool switcher
• CInput files
• DRun button
• EFile panel

New interface coming soon

This page shows the new SEGUI interface, which is in development. The current release (v1.1.3) looks different, and features marked In development are not available in it yet.

Concatenate multiple alignments into a single alignment with partition output.

Steps

1. Select Alignments in the navigation bar A.
2. Open Concatenate alignments from the tool list on wide windows, or select the tool name B at the top of the page to switch tools.
3. Add the input files C with Browse files, Browse folder, or Open archive. SEGUI searches a folder and its subfolders for files that match the tool's input format. See file input for mobile options.
4. The Input tab of the file panel E lists the input files. On phones and narrow windows, open it with the files button next to the tool name. To remove files from the list, choose Select, pick the files, and select Remove. The files stay on your device.
5. Select input format (optional). See the supported file extensions for the list of supported extensions for alignment files.
6. Select Browse under Select output directory to choose the output folder. On phones and tablets, enter a Directory name instead; SEGUI saves it in the app's own folder.
7. Set the prefix for the output file.
8. Set the output format.
9. Set the partition format (optional).
10. Select the run button D, labeled Concatenate, to start the task.
11. Export or share the output (optional). See exporting output.

Prefix

The app will use the prefix to name the output file. In the CLI version, the app has a default prefix. However, for the GUI version, you need to set the prefix manually. The prefix will be used as the output file name for the concatenated alignment and the partition file.

For example, if you set the prefix to concat, for nexus output and RAxML partition, the app will create two files: concat.nex and concat_partitions.txt.

Output format

The app supports FASTA, NEXUS, and PHYLIP output formats. By default, it writes non-interleaved output. To write interleaved output, select Advanced options and turn on Set interleaved format.

Partition format

The app supports Charset, NEXUS, and RAxML. The charset option only works when the output is NEXUS. For codon partitions, select Advanced options and turn on Set codon model partition.

Output file

• Concatenated alignment file
• Partition file (optional)

For charset partition, the partition will be in the same file as the alignment.