Alignment Splitting

Split an alignment into multiple alignments based on partition information.

Steps

Install PySEGUL using pip if you haven’t done it yet

pip install pysegul

Create a new Python script, import the library, and write python code

import pysegul

def split_alignment():
    input_alignment = 'tests/split-data/split-data.nex'
    input_format = 'nexus'
    datatype = 'dna'
    partition_format = 'nexus'
    output_format = 'fasta'
    # Check the partition before splitting. Set to False to skip checking.
    check_partition = True
    input_partition = 'tests/split-data/split-data_partition.nex'
    output_dir = 'tests/output'
    split = pysegul.AlignmentSplitting(
        input_alignment,
        input_format,
        datatype,
        output_dir,
        output_format,
        partition_format,
        check_partition,
        input_partition = input_partition
        )
    split.split()

If input_partition is not set, PySEGUL reads the partition from the input alignment.

Note

In PySEGUL 0.4.1 and earlier, check_partition is inverted: True skips partition checking. The upcoming release fixes it.