| name | fasttree |
| description | FastTree — approximately-maximum-likelihood trees for large alignments. Use when: (1) Draft phylogenies from big MSAs, (2) Quick topology screens before IQ-TREE, (3) Resource-limited exploratory MAG trees. Upstream: http://www.microbesonline.org/fasttree/. For final ML trees prefer iqtree. Route via phylogenomics.
|
| license | MIT |
| category | analysis-tools |
| tags | ["FastTree","phylogeny","approximate-ML","tree"] |
| upstream | http://www.microbesonline.org/fasttree/ |
| stage | taxonomy |
FastTree
Upstream: http://www.microbesonline.org/fasttree/ ·
often packaged as fasttree / FastTreeMP (bioconda)
Citation
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum
evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol.
26, 1641–1650 (2009). https://doi.org/10.1093/molbev/msp077
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 — approximately
maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
https://doi.org/10.1371/journal.pone.0009490
See also docs/references.md.
Analytical thinking
FastTree trades some accuracy for speed on large MSAs — ideal for
exploratory MAG/marker trees and PhyloPhlAn-scale drafts. For manuscript
figures and formal support values, re-infer with iqtree.
| vs | Prefer FastTree when |
|---|
iqtree | Huge MSA / quick topology / limited CPU |
| Distance-only trees | You still want approximate ML |
Always state FastTree vs IQ-TREE in Methods if both appear.
How to run
FastTreeMP -lg < markers.fa > temp/fasttree/tree.nwk
FastTreeMP -gtr -nt < markers.fna > temp/fasttree/tree.nwk
Decision tree
Tree speed vs rigor?
├─ Screen / huge alignment → fasttree
├─ Final ML + UFBoot → iqtree
└─ Full MAG phylogenomics workflow → phylophlan
Related skills
phylogenomics · iqtree · phylophlan · gtdbtk · mag-qc ·
tool-selection
