FigTree protocols

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Associated diseases

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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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  • person_outline Andrew Rambaut <>

FigTree in pipelines

 (445)
2018
PMCID: 5749770
PMID: 29293630
DOI: 10.1371/journal.pone.0190340

[…] []. metapiga calculations were stopped when the mean relative error of 10 consecutive consensus trees stayed below 5% using trees sampled every five generations. consensus trees were visualized in figtree v.1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/). reference strains for genotype 1a (genbank accession numbers af009606, ef407457, hq850279, m62321 and m67463) and for genotype 4d […]

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: 5769553
PMID: 29335015
DOI: 10.1186/s13071-018-2615-0

[…] to generate a convergence diagnostic. the final trees presented here are the consensus between the two final trees generated for each gene. results from all phylogenetic analyses were viewed in figtree v.1.4.2 []. proseq v.2.91 [] and arlequin v.3.11 [] software were used to obtain pairwise estimates of population differentiation []. the comparison of genetic distances, estimated […]

2018
PMCID: 5773221
PMID: 29346424
DOI: 10.1371/journal.ppat.1006754

[…] laboratory hiv sequence database (http://www.hiv.lanl.gov) was generated using muscle [, ]. neighbor joining and maximum likelihood trees were constructed with seaview 4 [] and visualized with figtree 1.4.2. genetic distance analysis within each sample were conducted using mega 6 [] and is expressed as substitutions per nucleotide (s/nt). the number of unique sequences was identified […]

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

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


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FigTree in publications

 (2434)
PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18

[…] and at=cg]) with unequal base frequencies, using empirical base frequencies and the freerate model of heterogeneity across sites, with three categories). the phylogenetic tree was visualized using figtree 1.4.3 (http://tree.bio.ed.ac.uk/software/figtree) and adobe illustrator., all mutant alleles were constructed in s. typhimurium lt2, s. saintpaul, and e. coli mg1655 with λ red recombineering […]

PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] merged two independent beast runs performed for 10,000,000 iterations with sampling every 1000 iterations. convergence of mcmc chains was assessed with tracer and analysis of consensus plotted with figtree yielded the same tree topology as found with raxml []., we assigned snvs in our call set to branches within this phylogeny using the ete toolkit in python []. for a given snv, we identify […]

PMCID: 5946514
PMID: 29747573
DOI: 10.1186/s12864-018-4762-2

[…] treeannotator component from the beast 2.3.0 package to obtain a consensus tree, the burn-in parameter for each chain was defined as 20%, the resulting phylogenetic tree file was visualized in the figtree program []., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: , electronic supplementary material , the online version of this article […]

PMCID: 5958175
PMID: 29780270
DOI: 10.3897/mycokeys.25.23836

[…] million generations. every 100th tree was saved into a file and aborting the analysis was set at the mean standard deviation < 0·01. tree topology of both ml and bi analyses was illustrated using figtree v.1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/)., two new dna sequences of mtssu and nulsu were generated for this study (table ). the alignment matrix contained 609 unambiguously […]

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

[…] partial 16s rrna gene sequences obtained in this study were added subsequently to the bayesian tree using the quick-add parsimony option in arb. the phylogenetic tree was visualized with itol and figtree, (fig. )., second, all obtained consensus sequences as well as the 16s rrna gene sequences of c. trachomatis a/har-13t (a_e17344.1), c. caviae strain: gp/ic (=atcc vr813) (d85708.1), n. […]


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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.