TreeFitter protocols

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TreeFitter statistics

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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 in pipeline

2012
PMCID: 3299616
PMID: 22214193
DOI: 10.1186/1471-2148-12-1

[…] hosts and parasites is permutated at random and used in conjunction with the other two matrices to produce a test statistic. we used 9999 permutations to calculate the test statistic. by comparison, treefitter is an event-based parsimony method that is useful for exploring the relationships between gene trees (parasite tree) and species trees (host tree). in the absence of reliable species […]


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TreeFitter in publications

 (8)
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 […]

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, […]

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 […]

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 […]

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 , : […]


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