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TreeFitter specifications


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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TreeFitter citations


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

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

[…] 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 […]


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

PMCID: 4521919
PMID: 26230508
DOI: 10.1371/journal.pone.0133655

[…] 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, […]


Evidence for Horizontal Transmission of Secondary Endosymbionts in the Bemisia tabaci Cryptic Species Complex

PMCID: 3538644
PMID: 23308142
DOI: 10.1371/journal.pone.0053084

[…] are more similar and if more codivergence events are present than would be expected by chance. commonly used tree based methods include reconciliation analysis (treemap) and generalized parsimony (treefitter) . treemap is used to find optimal reconstructions of the history of association by maximizing cospeciation events and minimizing host shifts. it uses the jungles analysis […]


Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

PMCID: 3299616
PMID: 22214193
DOI: 10.1186/1471-2148-12-1

[…] (fst) at the coi locus., a comparison between 42 terminal pollinator taxa with 26 ficus species resulted in non-significant congruence using parafit and under particular event cost schemes in treefitter tests. the application parafit tests a global null hypothesis that the association between the 'host' and 'parasite' phylogenies is independent. the global test of independence […]


Codivergence of Mycoviruses with Their Hosts

PMCID: 3146478
PMID: 21829452
DOI: 10.1371/journal.pone.0022252

[…] same co-phylogenetic tools for the same tasks. they were here applied to selected host-parasite datasets only, depending on the results of the parafit tests and the parameter sensitivity analysis., treefitter uses generalized parsimony to explore different cost combinations for each of the four types of events that might occur in the natural history of associated groups of organisms , : […]


Coevolution between a Family of Parasite Virulence Effectors and a Class of LINE 1 Retrotransposons

PMCID: 2759079
PMID: 19829700
DOI: 10.1371/journal.pone.0007463

[…] of the codivergence events was determined by generating 99 random te1a trees and determining how many of those supported solutions had as many codivergence events as the observed avrk1 tree . treefitter 1.0 was used for parsimony-based tree fitting. the significance of the results was tested by performing 1,000 random permutations of the te1a tree terminals., e. pisi (birmingham isolate, […]

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