TKF: Pairwise Distance Estimation with TKF91 and TKF92 Model

Pairwise evolutionary distance estimation between protein sequences with the TKF91 and TKF92 model, which consider all the possible paths of transforming from one sequence to another.

Install the latest version of this package by entering the following in R:
install.packages("TKF")
AuthorGe Tan <ge.tan09@imperial.ac.uk>
Date of publication2015-04-18 14:29:04
MaintainerGe Tan <ge.tan09@imperial.ac.uk>
LicenseGPL-2
Version0.0.8

View on CRAN

Files

inst
inst/TestData
inst/TestData/pair2.fasta
inst/TestData/pair1.fasta
inst/TestData/testSeqs.fasta
inst/buildMatrix
inst/buildMatrix/buildGonnet.R
inst/extdata
inst/extdata/pair1.fasta
inst/extdata/daymatrix.txt
inst/extdata/testSeqs.fasta
inst/extdata/pair.fasta
inst/extdata/testSet.fasta
inst/makePackage
inst/makePackage/TKF.txt
inst/unitTests
inst/unitTests/test_TKF92.R inst/unitTests/test_TKF92HG.R inst/unitTests/test_TKF91.R
inst/oldScripts
inst/oldScripts/dynprog_TKF92.c
inst/oldScripts/dynprog_TKF91.c
inst/oldScripts/TKF.r
tests
tests/runTests.R
src
src/matrix.c
src/Makevars
src/TKF91.h
src/MathFunctions.h
src/MathFunctions.c
src/TKF92HG.h
src/TKF92.h
src/R_init_TKF.c
src/TKF91.c
src/TKF92.c
src/Makevars.win
src/matrix.h
src/TKF92HG.c
NAMESPACE
data
data/GONNETBF.rda
data/GONNET.rda
R
R/ScoringMatrix.R R/TKF92HG.R R/MinSqTree.R R/TKF92.R R/TKF91.R
MD5
DESCRIPTION
man
man/PAMn.Rd man/GONNET.Rd man/TKF92HG.Rd man/optim.phylo.wls.Rd man/AAToInt.Rd man/TKF91.Rd man/TKF92.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.