Alignment Unalignment

Convert alignments to unaligned sequences by removing gaps and missing data. The output format can be fasta or fasta-int (interleaved).

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 unalign_alignments():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_dir = 'tests/output'
    unalign = pysegul.AlignmentUnalignment(
        input_format,
        datatype,
        output_dir,
        # Optional. Default: 'fasta'
        output_fmt='fasta',
        )
    unalign.from_dir(input_dir)

To use a list of files, call from_files instead of from_dir:

unalign.from_files(['tests/align-data/locus1.nex', 'tests/align-data/locus2.nex'])