Alignment Concatenation

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 concat_alignments():
    input_dir = 'tests/data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    partition_format = 'raxml'
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.AlignmentConcatenation(
        input_format,
        datatype,
        output_dir,
        output_format,
        partition_format,
        prefix
        )
    concat.from_dir(input_dir)

You can also input the alignment paths in a list directly instead of using a directory. Replace the input_dir with input_files and provide a list of paths. Then, call the from_files method instead of from_dir.

import pysegul

def concat_alignments():
    input_path = ['tests/data/alignment1.nex', 'tests/data/alignment2.nex']
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    partition_format = 'raxml'
    prefix = 'concatenated'
    output_dir = 'tests/output'
    concat = pysegul.AlignmentConcatenation(
        input_format,
        datatype,
        output_dir,
        output_format,
        partition_format,
        prefix
        )
    concat.from_files(input_path)