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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 […]

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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).

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