Skip to main content

Alignment Filtering

Filter an alignments. Available filtering options:

  • Alignment length
  • Parsimony informative sites
  • Percent parsimony informative sites
  • Taxon completeness

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 filter_alignments():
    input_dir = 'tests/align-data'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'nexus'
    is_concat = False
    output_dir = 'tests/output'
    filter = pysegul.AlignmentFiltering(
        input_format,  
        datatype, 
        output_dir, 
        output_format,
        is_concat
        )
    filter.input_dir = input_dir
    # For filtering by alignment length
    filter.minimal_length(8)
    # For filtering by parsimony informative sites
    filter.percent_informative(0.5)
    # For filtering by percent parsimony informative sites
    filter.percent_informative(0.5)
    # For filtering by minimal informative sites
    filter.minimal_parsimony_inf(4)
    # For filtering by taxon completeness
    filter.minimal_taxa(0.5)