This repository provides an easy-to-use Python-based pipeline for reconstructing phylogenetic trees from whole bacterial genomes. It automates the process of identifying orthologous single-copy genes, aligning sequences, trimming alignments, and generating a concatenated supermatrix ready for phylogenetic analysis. The pipeline requires only .fasta
bioinformatics supermatrix phylogenetics comparative-genomics comparative-genomics-studies phylogeny whole-genome-sequencing whole-genome evolutionary-biology concatination bacterial-genomics
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Updated
Sep 5, 2025 - Python