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Alignment Splitting

Split alignments into multiple files based on the partition.

Steps​

  1. Select the Alignment button from the navigation bar.
  2. Select Split alignments from the dropdown menu.
  3. Add the input files by clicking the Add file button. On desktop platforms, you can also input a directory by clicking the Add directory button. The app will look for matching files in the directory.
  4. Select the output directory by clicking the Add directory button.
  5. Input alignment partition.
  6. Add the output directory by clicking the Add directory button.
  7. Add prefix for the output files.
  8. Add output format.
  9. Click the Run button 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:

  1. First partition position starts with 1.
  2. 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.