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The Phylogenetic Methods skill provides a comprehensive framework for implementing computational biology workflows, specifically focusing on evolutionary tree reconstruction. It guides users through the entire bioinformatics pipeline, from performing multiple sequence alignment (MSA) with tools like MUSCLE and MAFFT to calculating distance matrices using Jukes-Cantor or Kimura models. The skill includes implementation patterns for various algorithms ranging from fast distance-based methods like UPGMA to statistically rigorous approaches like Maximum Likelihood and Bayesian inference, while also supporting tree visualization and standard file formats like Newick and Nexus.
