Alignment Partition Conversion

Convert alignment partition data between different formats. Available partition formats:

RAxML
NEXUS
Charset

Charset is a nexus format that stores partition data in the same file as a NEXUS alignment.

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. Example:

import pysegul

def convert_partitions():
    input_paths = [
        'tests/partition-data/partition_codon.txt',
        'tests/partition-data/partition.txt'
        ]
    # Available input and output format values: raxml, nexus, charset.
    input_format = 'raxml'
    output_format = 'nexus'
    datatype = 'dna'
    # Check the partition before converting. Set to False to skip checking.
    check_partition = True
    output_dir = 'tests/output'
    convert = pysegul.PartitionConversion(
        input_format,
        datatype,
        output_dir,
        output_format,
        check_partition
        )
    convert.from_files(input_paths)