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.

Author
Ge Tan <ge.tan09@imperial.ac.uk>
Date of publication
2015-04-18 14:29:04
Maintainer
Ge Tan <ge.tan09@imperial.ac.uk>
License
GPL-2
Version
0.0.8

View on CRAN

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...

Files in this package

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