Alignment Trimming

Desktop

Phone

AAlignments tab
BTool switcher
CInput files
DRun button
EFile panel

Trim alignment sites based on the proportion of missing data or the number of parsimony informative sites.

Steps

Select Alignments in the navigation bar A.
Open Trim 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 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.
Select the input format (optional) and the data type.
Select the trimming method and enter its value.
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.
Select the output format. Turn on Set interleaved format to write interleaved output (optional).
Select the run button D, labeled Trim, to start the task.

Parameters

Maximal missing data per site

The app keeps sites whose proportion of missing data (- or ?) is at most the value. The input is a decimal number between 0 and 1. For example, 0.5 removes sites where more than half of the samples have missing data.

Parsimony informative sites

The app keeps sites with at least the given number of parsimony informative characters. The input is a whole number, such as 2.

Output

The trimmed alignments are written to a trimmed_alignments folder in the output directory. The app also writes trimming_summary.csv, which lists the number of sites in each alignment before and after trimming. Alignments with no remaining sites are not written.