Unalign Alignments

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.

Remove alignment gaps to produce unaligned sequences, for example to realign them with a different aligner.

Steps

1. Select Alignments in the navigation bar A.
2. Open Unalign sequences 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. Select the input format (optional) and the data type.
5. 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.
6. Turn on Set interleaved format to write interleaved FASTA (optional).
7. Select the run button D, labeled Unalign, to start the task.

Output

The app writes one FASTA file for each input alignment, named after the input file. Gap characters are removed from every sequence. The output is always FASTA because unaligned sequences cannot be stored in NEXUS or PHYLIP.