Alignment Summary

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.

Summary statistics for many alignments.

Steps

1. Select Alignments in the navigation bar A.
2. Open Summarize 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. 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.
5. Add prefix for the output files.
6. Turn on Summarize each locus separately to write a summary file for each alignment instead (optional).
7. Select the run button D, labeled Summarize, to start the task.

Output

The app have three output files:

1. Alignment summary: A summary of the input alignments written to a text file (default name: alignment_summary.txt).
2. Locus summary: A summary of each alignment/locus written to a csv file (default name: locus_summary.csv).
3. Taxon summary: A summary of each taxon written to a csv file (default name: taxon_summary.csv).

Per-locus summary

With Summarize each locus separately on, the app writes a taxon summary for each alignment instead of the combined summary files. The summary interval does not apply to this mode.

Prefix

The prefix is the name of the output files. For example, if the prefix is output, the app will generate output_locus_summary.csv, output_taxon_summary.csv, and so on.