"Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance"

This repository contains the analyses described in the article Molecular Biology and Evolution. September 2025

Data Summary

SupplementaryTable1.xlsx contains metadata and NCBI accession numbers for the genomes from western Washington State.

Directory Structure and Content

Within_Viral_Species_Analyses/

This folder includes:

Maximum Likelihood trees constructed with IQ-TREE from complete genomes or HN gene sequences (from both complete and HN-only sequences). File extension .treefile

BEAST2 phylodynamic analyses from complete genomes, considering gene partition, or V/P and HN genes codon partitions. File extension of the trees .tre, and BEAST2 log files detailing parameter sampling during MCMC runs in .log files.

Annotation files (*.txt) for visualizing associated metadata (sample origin, date) alongside the trees.

HPIV-2_p-distance.xlsx: Pairwise p-distance estimates between genotypes calculated using MEGA X, used to validate HPIV-2 genotype classification.

Within_Taxonomic_Family_Analyses/

This folder includes Phylogenetic trees based on amino acid alignments of viral proteins from representative species of the Paramyxoviridae family.

Alignments trimmed to remove regions with poor homology (see Trimmed_Alignment/).

Maximum Likelihood trees generated using IQ-TREE (see _rep1 to _rep3 folders). File extension .treefile

Bayesian inference trees generated using MrBayes (see mrbayes/ folder). File extension .tre

Annotation file (Tree_annotation.txt) allows integration of taxonomic metadata (genus, subfamily, species) into visualization tools.