Alignment Summary

Desktop

ABCDE

Phone

ABCDE

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

New interface in SEGUI v1.2.0

This page shows SEGUI v1.2.0, now on Google Play and rolling out to other stores. Earlier versions look different. Features marked Beta may still change.

Summary statistics for many alignments.

Steps

1. Select Alignments in the navigation bar A.
2. Open Summarize alignments from the tool picker B: the tool list on wide windows, or the tool name at the top of the page on phones.
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.
8. When the task finishes, the Workbench tab of the file panel E shows a Report card. Select View report to open the alignment report. You can also open alignment-report.json from the Output tab later.
9. Export or share the output (optional). See exporting output.

Output

The app writes four 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).
4. Alignment report: every statistic in one file (default name: alignment-report.json), which opens as the interactive alignment report.

The CSV files open in the table viewer, where you can sort and page through them.

Alignment report

The alignment report shows the summary as charts and tables. It works like the other summary reports. The tabs are:

• Overview: the dataset at a glance.
  • Dataset: taxa, loci, sites, missing data, and GC content for DNA, with the mean and range of locus length and taxa per locus.
  • Site types: conserved, variable, and parsimony informative sites, with their count, range per locus, and share of all sites. The chart compares each type's share of sites with its share of loci: loci that are fully conserved, or have any variable or informative site.
  • Matrix completeness: the loci that include at least each share of the taxa, from 100% down by the summary interval.
  • Characters: the count of each character across all alignments, including gaps (-) and missing data (?).
• Loci: every alignment. Bars plots one statistic per locus: taxa, sites, conserved, variable, or informative sites, missing data, or GC content. Turn on Highest first to order the bars by that statistic, so the longest or gappiest loci come first. Table lists every statistic, sortable by column, and Heatmap colors the same table by value in each column. Type in Filter by name to narrow both views. Select a bar or a row to open a locus; its values stay below the list.
• Taxa: every taxon across the alignments, the same way: the loci it appears in, its characters and missing characters, missing data, and GC content. Use it to find taxa missing from many loci.
• Distributions: histograms across loci of locus length, taxa per locus, and parsimony informative sites, and of missing data per locus and per taxon. Each gives the median. Hover over or touch a bar to see its range and count.

Per-locus summaries write no report. Open their CSV files in the table viewer instead.

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, output_alignment_summary.txt, and output_alignment-report.json.