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Protocols

FigTree specifications

Information


Unique identifier OMICS_04268
Name FigTree
Alternative name Fig Tree
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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Versioning


No version available

Maintainer


  • person_outline Andrew Rambaut

FigTree citations

 (3269)
call_split

Predictable Phenotypes of Antibiotic Resistance Mutations

2018
MBio
PMCID: 5954217
PMID: 29764951
DOI: 10.1128/mBio.00770-18
call_split See protocol

[…] GT 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. […]

library_books

Analysis of the canid Y chromosome phylogeny using short read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

2018
BMC Genomics
PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] e 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 all le […]

library_books

Architrypethelium murisporum (Ascomycota, Trypetheliaceae), a remarkable new lichen species from Thailand challenging ascospore septation as an indicator of phylogenetic relationships

2018
PMCID: 5958175
PMID: 29780270
DOI: 10.3897/mycokeys.25.23836

[…] 10 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/). […]

library_books

Global evolution and phylogeography of Brucella melitensis strains

2018
BMC Genomics
PMCID: 5946514
PMID: 29747573
DOI: 10.1186/s12864-018-4762-2

[…] he 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 []. […]

library_books

Conservation systematics of the shield backed trapdoor spiders of the nigrum group (Mygalomorphae, Idiopidae, Idiosoma): integrative taxonomy reveals a diverse and threatened fauna from south western Australia

2018
Zookeys
PMCID: 5956031
PMID: 29773959
DOI: 10.3897/zookeys.756.24397

[…] erations, with the first 10% of sampled trees discarded as ‘burnin’ ([burnin = 4000]). Summary statistics of estimated parameters, including ESS values, were assessed using Tracer Version 1.6 (), and FigTree Version 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/ [accessed March 2018]) was used to visualise the 50% majority-rule consensus tree (Fig. ). Conservation assessments. The conservation […]

library_books

Detection of Chlamydiaceae and Chlamydia like organisms on the ocular surface of children and adults from a trachoma endemic region

2018
Sci Rep
PMCID: 5943520
PMID: 29743637
DOI: 10.1038/s41598-018-23887-1

[…] The 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. hartmann […]

Citations

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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.