MAF Summary

Desktop

Phone

AGenomics tab
BTool switcher
CInput files
DRun button
EFile panel

Summarize Multiple Alignment Format (MAF) files: the number of blocks, the alignment length, how much of the reference genome each species covers, and the proportion of gaps.

Steps

Select Genomics in the navigation bar A.
Open Summarize MAF alignments from the tool list on wide windows, or select the tool name B at the top of the page to switch tools.
Add the MAF 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.
Set the reference species or the species to report (optional). By default, the reference is the species of the first sequence in the first block, and every species is reported.
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.
Add a prefix for the output files (optional). The default is maf_summary.
Select the run button D, labeled Summarize, to start the task.

Output

The app writes two CSV files, which you can open in the app's table viewer:

Per file (maf_summary_per_file.csv): one row per MAF file with the number of blocks and species, the alignment length, the reference bases covered, the mean block score, and the proportion of gaps.
Per species (maf_summary_per_species.csv): one row per species in each file with the number of blocks it appears in, its bases and gaps, and the share of reference bases it covers. With more than one file, rows with the path all combine every file.

See the CLI guide for a description of every column.