FastTree pipeline

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

 (20)
2018
PMCID: 5811012
PMID: 29438384
DOI: 10.1371/journal.pone.0192439

[…] on the 18s rrna gene was selected through a combination of gblocks [22] and manual editing to use for tree building using muscle [23]. approximate maximum likelihood trees were constructed using fasttree v2.1 [24] in ‘accurate mode’ (-mlacc 2-slowmmi) with the general time reversible model and pseudocounts (number of bootstrap = 1,000)., the growth of ochromonas sp. strain ccmp1393 […]

2018
PMCID: 5880011
PMID: 29606099
DOI: 10.1186/s12862-018-1161-x

[…] to the same sm gene) were then combined, aligned using muscle (v3.8.31) [35] and trimmed using trimal (version 1.2) [36] in automated mode (−automated1). the phylogenetic tree was constructed using fasttree (version 2.1.7) [37] under the ‘wag+cat’ model with 4 rounds of minimum evolution spr moves (−psr 4) and exhaustive ml nearest-neighbor interchanges (−mlacc 2, −slownni). branch support […]

2017
PMCID: 5557543
PMID: 28813463
DOI: 10.1371/journal.pone.0182749

[…] for large alignments of the selected sequences was built, under the general time reversible model of nucleotide substitutions and varying substitution rates across sites (gtr+nt), with the software fasttree v2.1.7 [32]. branch support was calculated by shimodaira-hasegawa-like local branch support (sh-like test), as implemented in fasttree. trees were visualized with figtree (v1.4.2) [33]. […]

2017
PMCID: 5562387
PMID: 29104426
DOI: 10.1177/1176934317724404

[…] sequences were discarded if they have the alignment with more than 10% gaps. based on the alignment of concatenation of the remaining orthologous sequences, a phylogenetic tree was generated using fasttree19,20 with 1000 resamples. the phylogenic tree (called the species tree) was used as a reference tree for later use and can be visualized by figtree v1.4.2 […]

2017
PMCID: 5600125
PMID: 28493321
DOI: 10.1111/mec.14176

[…] 1,585,605 bp. phylogenetic trees were constructed from a whole‐genome alignment of c. jejuni (n = 229) and c. coli (n = 55) isolates based on 103,878 and 806,657 variable sites, respectively, using fasttree (version 2) and an approximation of the maximum‐likelihood algorithm (kumar, stecher, & tamura, 2016; tamura, stecher, peterson, filipski, & kumar, 2013)., to minimize the effect […]

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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