FastTree statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool FastTree

Tool usage distribution map

This map represents all the scientific publications referring to FastTree per scientific context
info info

Associated diseases

This word cloud represents FastTree usage per disease context

Popular tool citations

chevron_left Phylogenetic inference chevron_right
Want to access the full stats & trends on this tool?


FastTree specifications


Unique identifier OMICS_14703
Name FastTree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, PHYLIP
Output format NEWICK
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 2.1.9
Stability Stable
Source code URL
Maintained Yes




No version available



  • person_outline Morgan Price

Publications for FastTree

FastTree citations


Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

BMC Genomics
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] reesei and Ustilago maydis, 1032 single copy genes shared by all genomes were selected by orthofinder and aligned with mafft (mafft-linsi-anysymbol) [, ]. The phylogenomic tree was constructed using FastTree based on the alignments of single-copy ortholog families with approximately-maximum-likelihood model and bootstrap 100 []. […]


Detection of Chlamydiaceae and Chlamydia like organisms on the ocular surface of children and adults from a trachoma endemic region

Sci Rep
PMCID: 5943520
PMID: 29743637
DOI: 10.1038/s41598-018-23887-1

[…] ces were aligned using MAFFT v7.309. Jalview v2.10.1 was used to trim the alignment and to look for reverse complemented sequences. Maximum likelihood-based phylogenetic analyses were performed using FastTree 2.1 software (with parameters “-nt -gtr -spr 4 -mlacc 2 -slownni”). The phylogenetic representation was rerooted at the midpoint using Archaeopterix v0.9920 and displayed with FigTree v1.4.2 […]


Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] workflow, representative sequences from each OTU were selected and aligned against the Greengenes database gg_13_8 preclustered at 85% identity using PyNAST [] and used to build a tree using FastTree []. The OTU matching to chloroplasts of plant origin (“Streptophyta”) based on Greengenes taxonomic classification was manually removed. To improve taxonomic classification of the OTUs, taxon […]


Migratory Whooper Swans Cygnus cygnus Transmit H5N1 Virus between China and Mongolia: Combination Evidence from Satellite Tracking and Phylogenetics Analysis

Sci Rep
PMCID: 5935751
PMID: 29728621
DOI: 10.1038/s41598-018-25291-1
call_split See protocol

[…] er for Biotechnology Information (NCBI) as of 10 November 2016. Sequences were aligned with MAFFT v7.127b and trimmed to a length of 1716 bp. An approximate maximum likelihood tree was constructed by FastTree v2.1.4 as the setting of GTR + Gamma with SH-like local-bootstrap support values to estimate the reliability of each split in the tree. The tree was rooted at A/goose/Guangdong/1/96 and struc […]


Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia

PLoS One
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860
call_split See protocol

[…] g created a genome-wide multiple sequence alignment (>2.8 million positions) of all included genomic sequences [], from which an approximately-maximum-likelihood phylogenetic tree was generated using FastTree v2.1.10 [] and displayed with Dendroscope v3.5.9 []. Because no full-length, polished genomic sequences of USA100 were available, we corroborated results by generating trees using as referenc […]


High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

Front Microbiol
PMCID: 5943533
PMID: 29774020
DOI: 10.3389/fmicb.2018.00887

[…] d on nucleotide sequences. The first sequence within each OTU cluster was picked as a representative sequence. The representative sequences were aligned with MUSCLE and used to construct a tree using FastTree (). Representative sequences were checked by translating into amino acid sequences with CLC Sequence Viewer 7, and further confirmed by protein annotation with NCBI’s Conserved Domain Databas […]

Want to access the full list of citations?
FastTree institution(s)
Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA; Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Lab, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA
FastTree funding source(s)
This work was supported by a grant from the US Department of Energy Genomics: GTL program (DE-AC02-05CH11231).

FastTree reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FastTree