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.

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

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Files

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

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