Sequence Filtering

Desktop

Phone

ASequences tab
BTool switcher
CInput files
DRun button
EFile panel

Remove sequences inside each file based on their length or proportion of gaps. Unlike alignment filtering, which keeps or drops whole alignments, this task keeps or drops individual sequences.

Steps

Select Sequences in the navigation bar A.
Open Filter sequences 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 filtering 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 Filter, to start the task.

Parameters

Minimal sequence length

The app removes sequences with fewer non-gap characters than the value. The input is a whole number, such as 100.

Maximal sequence length

The app removes sequences with more non-gap characters than the value. The input is a whole number, such as 5000.

Maximal proportion of gaps

The app removes sequences whose proportion of gaps (- or ?) is greater than the value. The input is a decimal number between 0 and 1, such as 0.3.

Output

The app writes one file for each input file, named after the input file, with the sequences that pass the filter.