PySEGUL

PySEGUL is a python bindings of the SEGUL high-performance and memory-efficient phylogenomic tools. It is well-suited for large-scale phylogenomic projects involving thousands of loci, but it is just as capable of handling small Sanger sequences effectively.

Learn more on using PySEGUL in the documentation.

Quick Start

pip install pysegul

To concatenate alignments:

import pysegul

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

if __name__ == '__main__':
    concat_alignments()