msa_utilities

This software is provided as documentation for the manuscript "Using Neisseria meningitidis genomic diversity to inform outbreak strain identification". It is provided as is, with no guarantee of usability, and considered public domain.

To prepare alignments for phylogenetic analysis, the following two scripts were called:

mask_mapped_aln.py: This generates a masked alignment file from the alignment file produced by snippy-clean_full_aln. It also produces an partition file for RAxML providing information for ascertainment bias correction.

mask_mapped_aln.py alignment_file

adjust_partition_size.py: To adjust the partition size in the ascertainment bias correction file for RAXML, so that it maps properly to the Gubbins filtered polymorphic sites file.

adjust_partition_size.py gubbins_filtered_polymorphic_sites partition_file

To create distance matricies from kSNP results and from phylogenetic trees produced by RAxML.

DistanceCalculator.py kSNP kSNP_result_directory or DistanceCalculator.py tree tree_file