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FastTree is a highly efficient, open-source bioinformatics software designed to infer approximately-maximum-likelihood phylogenetic trees from massive nucleotide or amino acid multiple sequence alignments (MSAs). While traditional Maximum Likelihood (ML) programs like RAxML or IQ-TREE search tree topologies exhaustively, FastTree sacrifices a minute amount of topological accuracy to run 100 to 1,000 times faster. This makes it the premier choice for ultra-large datasets containing up to 1 million sequences. How FastTree Works

FastTree optimizes both speed and memory using a distinctive three-stage heuristic process: GitHub Pages documentation