FastTree specifications

Information


Unique identifier OMICS_14703
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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Documentation


Maintainer


  • person_outline Morgan Price <>

FastTree articles

FastTree citations

 (32)
2018
PMCID: 5923487

[…] bagv isolates and bagv sequences previously available from spain (hq644143-4, kr108244-6), india (eu684972) and car (ay632545). tree was inferred using fasttree v2.1.7 (http://www.microbesonline.org/fasttree/) [26], where nucleotide substitution was modeled using general time-reversible with a proportion of invariant sites (gtr+i). nodes were labeled with local support values, […]

2018
PMCID: 5880011

[…] 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 […]

2018
PMCID: 5905574

[…] was performed using the trimal, which removes poorly aligned regions (capella et al. 2009). approximate maximum-likelihood phylogenetic trees were constructed using the wag substitution model in fasttree (price et al. 2010) and visualized with figtree-v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/; last accessed july 5, 2017)., for the comprehensive identification of homologous […]

2017
PMCID: 5701628

[…] for each gene was 260 bp for archaeal amoa, 480 bp for aob 16s rrna, and 445 bp for nitrospira nxrb. maximum likelihood trees were constructed for representative sequences of observed otus using fasttree v2.1.5 package (price et al., 2010) in geneious v8.1.8 (kearse et al., 2012), with jukes-cantor correction and 100 bootstrap replicates. although significant bootstrap values (>50) […]

2017
PMCID: 5562387

[…] 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 […]

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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