Files in heibl/polenta
Multiple Sequence Alignment with PASTA and GUIDANCE
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/HoT.R
R/HoT_in_GUIDANCE2.R
R/RcppExports.R
R/align_part_set.R
R/centroidDecomposition.R
R/clustalo.R
R/clustalw2.R
R/decomposePhyloRooted.R
R/deleteGaps_dev.R
R/equalSubtrees.R
R/extractMSA.R
R/filterMSA.R
R/guidance.R
R/guidance2.R
R/guidanceSA.R
R/msaBP.R
R/msaBP_nj_tree.R
R/msa_set_scoreR.R
R/msa_set_scoreSA.R
R/muscle.R
R/partitions.R
R/pasta.R
R/polenta-package.R
R/polenta.R
R/polentaAA-class.R
R/polentaAA.R
R/polentaDNA-class.R
R/polentaDNA.R
R/polenta_dev.R
R/reappendScores.R
R/reappendScores_dev.R
R/reappendScores_gen_dev.R
R/residue_score_heatmap.R
R/rev_DNA.R
R/scores.R
R/spanningTree.R
R/transitivityMerge.R
README.md
dep/guidance-dep.R
dep/guidance.R
dep/mafft_dev.R
dep/merge.R
dep/protein_sequences.R
dep/res_pair_score.R
dev/00.R
dev/DEV-decomposePhylo.R
dev/DEV-guidance.R
dev/DEV-pasta.R
dev/DEV-scores.R
dev/add_msa_par.cpp
dev/alignSubtree.R
dev/cAAbin.R
dev/compareMSAs.R
dev/data/AATF.fas
dev/data/base.msa_10.rda
dev/data/cortinarius_28s_ms.fas
dev/data/guide.msa_10.rda
dev/dep_Rcpp/add_msa.cpp
dev/dep_Rcpp/cmatrix.R
dev/dep_Rcpp/cmatrix_parallel.cpp
dev/dep_Rcpp/msa_recode.cpp
dev/dep_Rcpp/msa_set_scoreR_par.R
dev/dep_Rcpp/res_pair_hit.cpp
dev/dep_Rcpp/res_pair_hit_3d.cpp
dev/dep_Rcpp/res_pair_score.cpp
dev/dep_Rcpp/res_score.cpp
dev/dep_Rcpp/score_calculation_dep.cpp
dev/dep_Rcpp/score_parallel.cpp
dev/dep_Rcpp/score_parallel_alt2.cpp
dev/dep_Rcpp/scores.R
dev/dep_Rcpp/subsequent_score_calc.cpp
dev/devworkspace.rda
dev/gapbase_bin.R
dev/guidance_dev.R
dev/opal.merge.R
dev/power.R
dev/res_pair_score.R
dev/scores.rda
dev/semphy-DEV.R
dev/src/.gitignore
dev/test.fas
dev/test.pdf
doc/large_benchmark_sources
inst/extdata/BB30015.fasta
inst/extdata/BB50009.fasta
man/HoT.Rd
man/Hot_GUIDANCE2.Rd
man/align_part_set.Rd
man/centroidDecomposition.Rd
man/confidence.heatmap.Rd
man/decomposePhyloRooted.Rd
man/deleteGaps.Rd
man/equalSubtrees.Rd
man/extractMSA.Rd
man/filterMSA.Rd
man/guidance.Rd
man/guidance2.Rd
man/guidanceSA.Rd
man/msaBP.Rd
man/msaBP_nj_tree.Rd
man/msa_set_scoreR.Rd
man/msa_set_scoreSA.Rd
man/partitions.Rd
man/pasta.Rd
man/polenta.Rd
man/polentaAA-class.Rd
man/polentaAA.Rd
man/polentaDNA-class.Rd
man/polentaDNA.Rd
man/polenta_dev.Rd
man/reappendScores.Rd
man/reappendScores_dev.Rd
man/reappendScores_gen_dev.Rd
man/rev_DNA.Rd
man/scores.Rd
man/spanningTree.Rd
man/transitivityMerge.Rd
polenta.Rproj
src/RcppExports.cpp
src/score_calculation.cpp
