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perfectphyloR
View on CRAN: Click
here
Download and install perfectphyloR package within the R console
Install from CRAN:
install.packages("perfectphyloR")
Install from Github:
library("remotes")
install_github("cran/perfectphyloR") Install by package version:
library("remotes")
install_version("perfectphyloR", "0.2.1") Attach the package and use:
library("perfectphyloR")
Maintained by
Charith Karunarathna
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-07-18
Latest Update:
Description:
Reconstructs perfect phylogeny at a user-given focal point and to depict and test association in a genomic region based on the reconstructed partitions. Charith B Karunarathna and Jinko Graham (2019) .
How to cite:
Charith Karunarathna (2019). perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data. R package version 0.2.1, https://cran.r-project.org/web/packages/perfectphyloR. Accessed 02 Nov. 2026.
Previous versions and publish date:
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Other R packages that perfectphyloR depends,
imports, suggests or enhances
Functions, R codes and Examples using
the perfectphyloR R package
Some associated functions: HHGtest . MantelTest . RVcoeff . RVtest . RandIndex . RandIndexTest . assoTest . buildDend . checkCompatible . createHapMat . dCor . dCorTest . dendToNewick . distMatRcpp . ex_hapMatSmall_data . ex_hapMat_data . extractHaplos . findSNVs . fourGamete . getNextFromFocal . getNextLeftFocal . getNextRightFocal . getnSNVs . makeDend . makeNewickRec . makePartition . mantelStat . newNode . noVariation . orderColsAncestry . orderSNVs . perfectphyloR-package . performTest . phenoDist . plotDend . rdistMatrix . reconstructPP . reconstructPPregion . selectWindow . splitTips . subsetHapMat . tdend . testAssoDist . testDendAssoRI . vcftohapMat .
Some associated R codes: HHG_test.R . RV_test.R . RcppExports.R . association_tests.R . association_tests_utility_functions.R . build_dend.R . create_HapMat.R . dCor_test.R . ex_data.R . ex_small_data.R . find_SNV.R . find_SNV_utility_functions.R . make_dend.R . make_dend_utility_functions.R . mantel_test.R . order_SNV.R . order_SNV_utility_functions.R . phenoDist_data.R . plot_dend.R . rand_index_test.R . rdistMatrix.R . reconstructPPregion.R . reconstruct_PP.R . select_window.R . subset_hapMat.R . tdend_data.R . testDendAssoRI.R . vcf_to_hapMat.R . vcf_to_hapMat_utility_function.R . Full perfectphyloR package functions and examples
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