FigTree pipeline

FigTree specifications

Information


Unique identifier OMICS_04268
Name FigTree
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format Nexus, Newick
Output format PDF,SVG,PNG,JPEG
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.4.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andrew Rambaut <>

FigTree IN pipelines

 (325)
2018
PMCID: 5764404
PMID: 29324895
DOI: 10.1371/journal.ppat.1006780

[…] model with a gamma (γ) distribution of among-site rate variation. support for individual nodes was assessed using a bootstrap procedure with 100 replicates and phylogenetic trees were annotated in figtree (v1.4.3)., we thank the office of health protection (ohp), the communicable disease network australia (cdna) and the national notifiable disease surveillance system (nndss) for providing […]

2018
PMCID: 5776109
PMID: 29387045
DOI: 10.3389/fmicb.2017.02675

[…] et al., 2002), and the phylogenetic trees were inferred using maximum likelihood (jones et al., 1992). bootstrap values were calculated based on 100 replications. trees were adapted using the figtree program (v1.4.3.) (rambaut, 2009)., the metagenomic insert sequences from industry area 1 are shown in table 2 and were deposited in genbank under accession numbers mg585943 to mg585960. […]

2018
PMCID: 5778038
PMID: 29358662
DOI: 10.1038/s41598-018-19671-w

[…] method34 with 1000 bootstrap replicates35 for each analysis. pairwise deletion was employed to address alignment gaps and missing data., the trees were visualized and edited using the figtree program (http://tree.bio.ed.ac.uk/software/figtree/)., rna was extracted from the th and ta mycelia samples using the licl rna extraction protocol according to the method reported by oliveira […]

2018
PMCID: 5778038
PMID: 29358662
DOI: 10.1038/s41598-018-19671-w

[…] for each analysis. pairwise deletion was employed to address alignment gaps and missing data., the trees were visualized and edited using the figtree program (http://tree.bio.ed.ac.uk/software/figtree/)., rna was extracted from the th and ta mycelia samples using the licl rna extraction protocol according to the method reported by oliveira et al.36. the tri reagent solution (ambion) […]

2018
PMCID: 5787326
PMID: 29373979
DOI: 10.1186/s12985-018-0931-9

[…] the isolates. the appropriate nucleotide substitution model was selected by jmodeltest program version 2.1.4 [16]. the visualization and edition of the phylogenetic trees were performed using figtree v.1.4.1., a complete genome of the tospovirus tomato chlorotic spot virus (tcsv) was assembled (fig. 2). tospoviruses are compound by three single stranded-rnas within spherical particle […]

FigTree review

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Erica Souza

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Desktop
FigTree is software that allows to edit phylogenetic trees. The edition consists:
(i) Change the clade names, (ii) Modify the line colors and thickness, (iii) Change tree style, (iv) Show the bootstrap, posterior probability values, and node ages.
In addition, you cannot summarized and annotated trees produced by BEAST, for this you should use TreeAnnotator and LogCombiner. The software it is not exclusive for BEAST users, you can use it to visualize trees from: MrBayes, PhyML, RaxML and others softwares.