phylogenetics-tree-builder

# Phylogenetics Tree Builder Skill ## Purpose Enable phylogenetic analysis for constructing evolutionary trees, performing multiple sequence alignments, and assessing phylogenetic relationships. ## Capabilities - Multiple sequence alignment (MUSCLE, MAFFT) - Maximum likelihood tree construction - Bayesian phylogenetic inference - Bootstrap support calculation - Tree visualization and annotation - Molecular clock analysis ## Usage Guidelines - Align sequences before tree construction - Select appropriate substitution models - Calculate bootstrap support for branch confidence - Visualize trees with meaningful annotations - Consider molecular clock constraints when appropriate - Document methodology and parameters ## Dependencies - RAxML-NG - IQ-TREE - MrBayes - MAFFT - MUSCLE - FigTree ## Process Integration - 16S rRNA Microbiome Analysis (16s-microbiome-analysis) - Shotgun Metagenomics Pipeline (shotgun-metagenomics) - Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)