FastTree protocols

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FastTree specifications

Information


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 http://microbesonline.org/fasttree/FastTree.c
Maintained Yes

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Maintainer


  • person_outline Morgan Price <>

Publications for FastTree

FastTree in pipelines

 (230)
2018
PMCID: 5759035
PMID: 29354144
DOI: 10.3389/fpls.2017.02191

[…] alignments of cotu sequences using clustal omega v1.2.1 (sievers et al., ) with 1,000 iterations. a phylogenetic tree was constructed by maximum likelihood using qiime v1.8.0 (caporaso et al., ) and fasttree v2.1.3 (price et al., ). the tree was visualized using graphlan v0.9.7 (asnicar et al., )., the cbc dataset was cross-referenced with the sugarcane microbiome dataset (de souza et al., ) […]

2018
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] was performed using deblur (amir et al., ) to obtain putative error-free sequences from the original data. a phylogenetic tree was therefore built by making use of mafft (katoh and standley, ) and fasttree 2 (price et al., ) allowing computation of subsequent diversity metrics., alpha-diversity (within-sample species richness) and beta-diversity (between-sample community dissimilarity) […]

2018
PMCID: 5769542
PMID: 29337314
DOI: 10.1038/sdata.2017.203

[…] using trimal (v.1.2rev59; parameter: -automated1), and manually assessed. alignments for each set of markers were concatenated. a maximum likelihood tree using the lggamma model was generated using fasttree (v.2.1.10; parameters: -lg -gamma; supplementalinformation1-hugtree.newick.txt, supplementalinformation2-alttree.newick.txt, data citation 2). phylogenies were determined manually for 2,009 […]

2018
PMCID: 5785536
PMID: 29371626
DOI: 10.1038/s41467-017-02342-1

[…] 2.05 on the consensus sequences. global phylogenetic tree was constructed from a global alignment using mafft 7.310. the phylogenetic inference was made using approximate maximum likelihood with fasttree, under the gamma model of heterogeneity., in order to estimate the abundance and expression of each unigene in each sample, cleaned reads (from metagenomes and metatranscriptomes) […]

2018
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] of 70% using vsearch (). sequences were aligned with probcons () and reliable positions for phylogenetic reconstruction were manually selected. a maximum likelihood phylogeny was estimated with fasttree 2 ()., isothermal titration calorimetry (itc) experiments were carried out on a microcal peaq-itc system (malvern instruments ltd) in a buffer containing 25 mm hepes (ph 7.65), 150 mm nacl, […]


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FastTree in publications

 (1255)
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 []., gene family annotation for c. pseudoreteaudii […]

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

[…] 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 […]

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, […]

PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] 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 […]

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

[…] 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 […]


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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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