Comprehensive Supplementary Dataset: Viral Evolution Analyses Including Recombination, Molecular Clock, and Selection Pressure

This repository contains all supplementary materials that support the full
spectrum of viral evolutionary analyses in the study, including
recombination detection, temporal signal assessment, substitution rate
estimation, and positive selection detection across diverse viral taxa.
The dataset is divided into five subdirectories: Viruses – GenBank-derived
viral FASTA sequences parsed through custom scripts, serving as primary
data for downstream analyses. Scripts – A set of 23 Python scripts used
for sequence parsing, filtering, and analysis; details on usage are
provided in the thesis (Chapter 2, Table 2, Section 2.1.2). Recombination
– Spreadsheet summarising recombination signals per alignment, filtered by
temporal signal and taxonomy. Molecular Clock – MEGA-aligned files and
Newick trees used in TempEst analyses, along with temporal signal
statistics. Positive Selection – Input/output files from SLR runs,
including phylip alignments, tree files, and control files per virus;
accompanied by spreadsheets summarising sites under positive selection and
InterProScan annotations. This dataset provides the full methodological
foundation to replicate or extend the evolutionary analyses presented in
the project, which aims to understand how tempo and mode of evolution vary
across viral taxonomic structures and whether these patterns can serve as
taxonomic markers.Description