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Protocols

TreeFitter specifications

Information


Unique identifier OMICS_08813
Name TreeFitter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


TreeFitter citations

 (15)
library_books

Towards sub quadratic time and space complexity solutions for the dated tree reconciliation problem

2016
PMCID: 4875752
PMID: 27213010
DOI: 10.1186/s13015-016-0077-5

[…] e biological data considered have been applied to the validation of a number of coevolutionary analysis algorithms including TreeCollapse [] and RASCAL [], and includes the data sets used to validate TreeFitter [], ParaFit [], Tarzan [], CoRe-PA [], CoRe-ILP [], and Jane []. In total this data set contains 102 unique tanglegrams and is the largest single source of biological data sets for coevolut […]

library_books

Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage

2016
Front Genet
PMCID: 4802293
PMID: 27047538
DOI: 10.3389/fgene.2016.00035

[…] the two descendants (). In practice, this implies that dispersal and extinction events are underestimated (minimized) in event-based reconstructions. For example, under default cost assignments (; ), TreeFitter will recover the “single dispersal event” scenario, though the cost of the “high extinction asymmetry” scenario is only slightly higher (Figure ). One reason for this is that in event-based […]

call_split

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

2016
PMCID: 5804275
PMID: 29491928
DOI: 10.1093/cz/zow018
call_split See protocol

[…] text, the aim is to find a reconstruction of P and H that is consistent with the tip mapping ϕ and that minimizes the total cost of the events in the mapping. first proposed a reconstruction method (TreeFitter) that explicitly measured the fit between the data and a particular reconstruction in terms of the number of postulated specific evolutionary events. TreeFitter addressed for the first time […]

call_split

Host Jumps and Radiation, Not Co‐Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae

2015
PLoS One
PMCID: 4521919
PMID: 26230508
DOI: 10.1371/journal.pone.0133655
call_split See protocol

[…] pare a range of trees representing alternative hypotheses of host and parasite relationships and identify those elements of the reconstructions that are shared across combinations of trees, Icong [], TreeFitter 1.3.2 [], Tarzan v0.9 [], CoRe-PA 0.5.1 [], Jane 4 [], as well as a distance-based method, ParaFit []. Among them, Icong, TreeFitter, and Tarzan do not accept polytomies in topologies, and […]

call_split

An analysis of pterosaurian biogeography: implications for the evolutionary history and fossil record quality of the first flying vertebrates

2015
PMCID: 4536946
PMID: 26339122
DOI: 10.1080/08912963.2014.939077
call_split See protocol

[…] ate Cretaceous in age (Figures and ). This phylogeny is fully resolved apart from a single trichotomy linking the three terminals comprising Nyctosauridae. Cladistic biogeographical methods, such as Treefitter (see below), cannot deal with polytomies, so this trichotomy must be removed prior to analysis. All three of the nyctosaurid taxa occur in the Late Cretaceous, two in North America and one […]

call_split

Cophylogenetic relationships between Anicetus parasitoids (Hymenoptera: Encyrtidae) and their scale insect hosts (Hemiptera: Coccidae)

2013
BMC Evol Biol
PMCID: 3878026
PMID: 24365056
DOI: 10.1186/1471-2148-13-275
call_split See protocol

[…] 28S were created by collapsing all sequences from the same species using BioEdit 7.0.5, and used in the analysis of the congruence of parasite and host phylogenies. Several methods using TreeMap [,], TreeFitter [], Jane 4 [] and ParaFit [], are available to study the congruence between symbiont and host phylogenies. In the present study, three methods were used: a distance-based method called Para […]


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