c4da9a4824e432f847dd77fb03fc5796 *DESCRIPTION
dda2fbcc796f23d245d7e684cd6943a6 *NAMESPACE
9083446b9cadaaea59dd557141b219d9 *R/marginalRecon.R
365b44dd58f8c674cde39773f492a957 *R/modelAdequacy.R
9a86eb646ee1d1480ea97246eac4e3b8 *R/nzp.R
dafcb4cfc88297e5f41ffd4f64a70512 *R/plot.R
7fe7f3847b013d733cbc13b1897436f6 *R/selac.R
8e8523a9e59ba63ebc27fd3dc3e7c8f7 *R/selacSim.R
a8ab7814714e6892ea9a02ba15b42dd9 *R/selon.R
32b255f8c46edba90af879b54f7c52f5 *README.md
1993c47d726bb94219049559a1ecbc07 *data/archosaurs.rda
2ff654db9a16fb88a68494b6a7c1ece4 *data/non_zero_pos.rda
0e3b69c532b117a4ef22891c2ff9b3a5 *data/yeast.rda
3fac14ea35a20317e02fd55e689fe5e3 *inst/extdata/gene1Yeast.fasta
6a081857f78209f7d50698336e52ad7c *inst/extdata/rokasYeast.tre
8ec0bd66bb9b710b148f1a30f2d4b5b2 *man/GetAdequateManyReps.Rd
7ca18168db09fcbbb0171dca8fdd2019 *man/GetAdequateSelac.Rd
3e25f0a509deebe8a67830ee101f3edb *man/GetFunctionality.Rd
dacb43890d9373641985708734b341ad *man/GetMarginalAllGenes.Rd
630fb2f9dd530d34a9d05b5ba2e576df *man/GetPartitionOrder.Rd
50e94d628e8283307939c9e92603d5c9 *man/GetSelacPhiCat.Rd
b5a8b7a480800d6a64e0897952f7ef31 *man/GetSelacSiteLikelihoods.Rd
2fe0b85098a33360158c21c7e7da28ed *man/NucSimulator.Rd
cb0a6af201cbb67c3facac16ea645b15 *man/PlotEquilbriumCodonDistribution.Rd
68db23743acf2823e3ac51ec71f87109 *man/PlotExpectedFitness.Rd
afac3851dc0e867ce4d9d679b784b66e *man/PlotGeneSiteInfo.Rd
3bf7190b73a5aa9074972aca3d0c134b *man/PlotMutationFitnessSpectra.Rd
88b3a96fe5cb201d5411b6d3db853495 *man/PlotPerAAFitness.Rd
7d96e940d3548c854825655305bc83bb *man/SelacHMMOptimize.Rd
41bcbb70e8acf9f9ab62086256f9e046 *man/SelacHMMSimulator.Rd
620f3c4a13e430e3fb657bc3b0488014 *man/SelacOptimize.Rd
38db7b6aefbd21ba925b7bf950d99c35 *man/SelacSimulator.Rd
66eba98172ca4ddd780a9c84c5c991fc *man/SelacSimulatorEvolvingRates.Rd
22969e868ab7691c1a34ded94a9f8d09 *man/SelonHMMOptimize.Rd
e817668464e8da41e94d2c955fd71c82 *man/SelonOptimize.Rd
462371456e25a06656eac47290940ceb *man/SelonSimulator.Rd
c44350a56a1b51e6810812b916c23a72 *man/archosaur.Rd
9d6b6e75eddcb7815cf82eeeff19a9b5 *man/internal.Rd
bfa0feee1e4ab96acbe0c609f3013b37 *man/non_zero_pos.Rd
28c85c64ef30032f150eaf079346abc2 *man/yeast.Rd
fb0b77fc2982ac935ad2b36d1fe98854 *tests/testthat.R
3fac14ea35a20317e02fd55e689fe5e3 *tests/testthat/gene1Yeast.fasta
6a081857f78209f7d50698336e52ad7c *tests/testthat/rokasYeast.tre
a6ff2e3e5260356327310679e3c4170a *tests/testthat/test_likelihood.R
5fc26413eec64584adb180ff85208892 *tests/testthat/test_utility.R
