Alignment Splitting

Desktop

Phone

AAlignments tab
BTool switcher
CInput files
DRun button
EFile panel

Split alignments into multiple files based on the partition.

Steps

Select Alignments in the navigation bar A.
Open Split 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.
Under Input Partition, select the partition format, then select the partition file with Browse. Skip the file for a charset partition in the same NEXUS file as the alignment.
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.
Select the output format.
Select the run button D, labeled Split, to start the task.

Input Partition

The app supports input partition formats. The input partition format is the format of the partition file you want to split. Partition options include:

Charset: partition embedded in NEXUS sequence files
Nexus: partition file in NEXUS format
Raxml: partition file in RAxML format

It supports standard and codon model partitions. However, merged partitions are not supported. The partition format will include the datatype as below:

DNA, locus_1 = 1-100
DNA, locus_2 = 101-150
DNA, locus_3 = 151-200

Unsupported partition format examples:

DNA, part1 = 1-100, 201-300
DNA, part2 = 101-200

Check Partition for Errors

The app checks for the following rules:

First partition position starts with 1.
The next partition is next number after the end of the previous partition. If codon model, it will check the next locus applies the rule.

Prefix

The prefix is the name of the output files. For example, if the prefix is output, the app will generate output_locus1, output_locus2, and so on.