veryfasttree

Fast phylogenetic tree inference for large taxonomic datasets

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Efficient phylogenetic tree inference for massive taxonomic datasets

fasttreeFastTreeFastTreeMP

Build a phylogenetic tree from a protein sequence alignment$ fasttree -quiet proteins.fa > tree.nwk

Infer tree from nucleotide sequences with WAG model and bootstrap support$ FastTree -nt -boot 100 sequences.fasta > output_tree.nwk

Run multi-threaded tree inference on large alignment with optimization$ FastTreeMP -nt -gamma -spr 4 large_alignment.fa > final_tree.nwk