TKF: Pairwise Distance Estimation with TKF91 and TKF92 Model
Version 0.0.8

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.

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TKF")

Popular man pages

AAToInt: AA, DNA, RNA character set
GONNET: The GONNET AA matrix
optim.phylo.wls: Phylogeny inference using the weighted least squares method
PAMn: PAM and Dayhoff matrices calculation
TKF91: Evolutionary distance estimation with TKF91 model
TKF92: Evolutionary distance estimation with TKF92 model
TKF92HG: Evolutionary distance estimation with TKF92 model considering...
See all...

All man pages Function index File listing

Man pages

AAToInt: AA, DNA, RNA character set
GONNET: The GONNET AA matrix
optim.phylo.wls: Phylogeny inference using the weighted least squares method
PAMn: PAM and Dayhoff matrices calculation
TKF91: Evolutionary distance estimation with TKF91 model
TKF92: Evolutionary distance estimation with TKF92 model
TKF92HG: Evolutionary distance estimation with TKF92 model considering...

Functions

AACharacterSet Man page
AAGapCharacterSet Man page
AAToInt Man page Source code
AmbiguousAACharacterSet Man page
AmbiguousAAGapCharacterSet Man page
DNACharacterSet Man page
DNAGapCharacterSet Man page
Dayhoffn Man page Source code
GONNET Man page
GONNETBF Man page
PAMn Man page Source code
RNACharacterSet Man page
RNAGapCharacterSet Man page
TKF91 Man page Source code
TKF91Pair Man page Source code
TKF92 Man page Source code
TKF92HG Man page Source code
TKF92HGPair Man page Source code
TKF92Pair Man page Source code
ls.tree Source code
optim.phylo.wls Man page Source code
validMatrix Source code
validateBF Source code
validatePAMMatrix Source code

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
TKF documentation built on May 19, 2017, 8:25 p.m.