Files in PoonLab/clustuneR
Molecular clustering implementation and predictive optimization
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/analysis.R
R/data.R
R/generate.data.R
R/graph-clustering.R
R/graph-setup.R
R/sequence-setup.R
R/tree-clustering.R
R/tree-setup.R
README.Rmd
README.md
README_files/figure-gfm/unnamed-chunk-10-1.png
README_files/figure-gfm/unnamed-chunk-4-1.png
clustuneR.Rproj
data/alignment.ex.RData
data/cluster.ex.RData
data/cn.fasta
data/extended.tree.ex.RData
data/full.tree.ex.RData
data/graph.ex.RData
data/na.fasta
data/na.log
data/na.nwk
data/old.tree.ex.RData
data/seq.info.ex.RData
data/st.fasta
data/tn.fasta
data/tree-example.RData
examples/component.cluster_ex.R
examples/create.graph_ex.R
examples/extend.tree_ex.R
examples/fit.analysis_ex.R
examples/get.AIC_ex.R
examples/multi.cluster_ex.R
examples/parse.headers_ex.R
examples/step.cluster_ex.R
inst/exdata/IQTREE_log_ex.txt
inst/exdata/RAxML_log_ex.txt
inst/guppy.Darwin
inst/guppy.Linux
inst/pplacer.Darwin
inst/pplacer.Linux
man/alignment.ex.Rd
man/annotate.growth.Rd
man/annotate.nodes.Rd
man/annotate.paths.Rd
man/cluster.ex.Rd
man/component.cluster.Rd
man/extend.tree.Rd
man/extended.tree.ex.Rd
man/fit.analysis.Rd
man/fit.decay.Rd
man/full.tree.ex.Rd
man/generate.all.Rd
man/generate.cluster.Rd
man/generate.graph.Rd
man/generate.seq.info.Rd
man/generate.tree.Rd
man/get.AIC.Rd
man/graph.ex.Rd
man/import.tree.Rd
man/minimum.retrospective.edge.Rd
man/mono.pat.cluster.Rd
man/multi.cluster.Rd
man/old.tree.ex.Rd
man/parse.headers.Rd
man/read.edges.Rd
man/run.pplacer_guppy.Rd
man/seq.info.ex.Rd
man/step.cluster.Rd
man/taxit.create.Rd
man/translate.log.Rd
tests/testthat.R
tests/testthat/growth.tre
tests/testthat/growth2.tre
tests/testthat/helper_iss22.R
tests/testthat/test-analysis.R
tests/testthat/test-graph-clustering.R
tests/testthat/test-graph-setup.R
tests/testthat/test-newseq.fasta
tests/testthat/test-oldseq.fasta.log
tests/testthat/test-oldseq.fasta.treefile
tests/testthat/test-sequence-setup.R
tests/testthat/test-tree-clustering.R
tests/testthat/test-tree-setup.R
tests/testthat/test.fasta
tests/testthat/test.tn93.csv
tests/testthat/test2-old.fasta.log
tests/testthat/test2-old.fasta.treefile
tests/testthat/test2.fasta
tests/testthat/test2.tn93.csv
