LICENSE
README.md
decompose.py
make_gene_folder.py
run_treeshrink.py
setup.py
R_scripts/Rfunctions.R
R_scripts/find_d.R
R_scripts/find_outliers.R
R_scripts/find_outliers_IQR.R
R_scripts/find_outliers_IQR.log.R
R_scripts/find_outliers_adjIQR.R
R_scripts/find_outliers_bootliers.R
R_scripts/find_threshold.R
R_scripts/find_threshold_IQR.R
R_scripts/find_threshold_hnorm.R
R_scripts/find_threshold_kernel.R
R_scripts/find_threshold_lkernel.R
R_scripts/find_threshold_lnorm.R
R_scripts/find_threshold_loglnorm.R
R_scripts/plot_allgenes.R
R_scripts/plot_pergene.R
R_scripts/plot_perspecies.R
R_scripts/plot_threshold.R
Rlib/BMS/CITATION
Rlib/BMS/DESCRIPTION
Rlib/BMS/INDEX
Rlib/BMS/NAMESPACE
Rlib/BMS/Meta/Rd.rds
Rlib/BMS/Meta/data.rds
Rlib/BMS/Meta/demo.rds
Rlib/BMS/Meta/features.rds
Rlib/BMS/Meta/hsearch.rds
Rlib/BMS/Meta/links.rds
Rlib/BMS/Meta/nsInfo.rds
Rlib/BMS/Meta/package.rds
Rlib/BMS/Meta/vignette.rds
Rlib/BMS/R/BMS
Rlib/BMS/R/BMS.rdb
Rlib/BMS/R/BMS.rdx
Rlib/BMS/data/datafls.rda
Rlib/BMS/demo/BMS.growth.R
Rlib/BMS/doc/bmasmall.bib
Rlib/BMS/doc/bms.R
Rlib/BMS/doc/bms.Rnw
Rlib/BMS/doc/bms.pdf
Rlib/BMS/doc/index.html
Rlib/BMS/help/AnIndex
Rlib/BMS/help/BMS.rdb
Rlib/BMS/help/BMS.rdx
Rlib/BMS/help/aliases.rds
Rlib/BMS/help/paths.rds
Rlib/BMS/html/00Index.html
Rlib/BMS/html/R.css
TREESHRINK.egg-info/PKG-INFO
TREESHRINK.egg-info/SOURCES.txt
TREESHRINK.egg-info/dependency_links.txt
TREESHRINK.egg-info/top_level.txt
dendropy/__init__.py
dendropy/__main__.py
dendropy/calculate/__init__.py
dendropy/calculate/combinatorics.py
dendropy/calculate/mathfn.py
dendropy/calculate/phylogeneticdistance.py
dendropy/calculate/popgenstat.py
dendropy/calculate/probability.py
dendropy/calculate/profiledistance.py
dendropy/calculate/statistics.py
dendropy/calculate/treecompare.py
dendropy/calculate/treemeasure.py
dendropy/calculate/treescore.py
dendropy/calculate/treesum.py
dendropy/dataio/__init__.py
dendropy/dataio/fastareader.py
dendropy/dataio/fastawriter.py
dendropy/dataio/ioservice.py
dendropy/dataio/newick.py
dendropy/dataio/newickreader.py
dendropy/dataio/newickwriter.py
dendropy/dataio/newickyielder.py
dendropy/dataio/nexmlreader.py
dendropy/dataio/nexmlwriter.py
dendropy/dataio/nexmlyielder.py
dendropy/dataio/nexusprocessing.py
dendropy/dataio/nexusreader.py
dendropy/dataio/nexuswriter.py
dendropy/dataio/nexusyielder.py
dendropy/dataio/phylipreader.py
dendropy/dataio/phylipwriter.py
dendropy/dataio/tokenizer.py
dendropy/dataio/xmlprocessing.py
dendropy/datamodel/__init__.py
dendropy/datamodel/basemodel.py
dendropy/datamodel/charmatrixmodel.py
dendropy/datamodel/charstatemodel.py
dendropy/datamodel/datasetmodel.py
dendropy/datamodel/taxonmodel.py
dendropy/datamodel/treecollectionmodel.py
dendropy/datamodel/treemodel.py
dendropy/interop/__init__.py
dendropy/interop/ape.py
dendropy/interop/biopython.py
dendropy/interop/entrez.py
dendropy/interop/ete.py
dendropy/interop/gbif.py
dendropy/interop/genbank.py
dendropy/interop/muscle.py
dendropy/interop/paup.py
dendropy/interop/raxml.py
dendropy/interop/rspr.py
dendropy/interop/rstats.py
dendropy/interop/seqgen.py
dendropy/legacy/__init__.py
dendropy/legacy/coalescent.py
dendropy/legacy/continuous.py
dendropy/legacy/ncbi.py
dendropy/legacy/popgensim.py
dendropy/legacy/popgenstat.py
dendropy/legacy/reconcile.py
dendropy/legacy/seqmodel.py
dendropy/legacy/seqsim.py
dendropy/legacy/treecalc.py
dendropy/legacy/treemanip.py
dendropy/legacy/treesim.py
dendropy/legacy/treesplit.py
dendropy/legacy/treesum.py
dendropy/mathlib/__init__.py
dendropy/mathlib/mathfn.py
dendropy/mathlib/probability.py
dendropy/mathlib/statistics.py
dendropy/model/__init__.py
dendropy/model/birthdeath.py
dendropy/model/coalescent.py
dendropy/model/continuous.py
dendropy/model/discrete.py
dendropy/model/multispeciescoalescent.py
dendropy/model/parsimony.py
dendropy/model/protractedspeciation.py
dendropy/model/reconcile.py
dendropy/model/treeshape.py
dendropy/simulate/__init__.py
dendropy/simulate/charsim.py
dendropy/simulate/popgensim.py
dendropy/simulate/treesim.py
dendropy/utility/__init__.py
dendropy/utility/bibtex.py
dendropy/utility/bitprocessing.py
dendropy/utility/cli.py
dendropy/utility/constants.py
dendropy/utility/container.py
dendropy/utility/debug.py
dendropy/utility/deprecate.py
dendropy/utility/error.py
dendropy/utility/filesys.py
dendropy/utility/messaging.py
dendropy/utility/metavar.py
dendropy/utility/processio.py
dendropy/utility/terminal.py
dendropy/utility/textprocessing.py
dendropy/utility/timeprocessing.py
dendropy/utility/urlio.py
dendropy/utility/vcsinfo.py
dendropy/utility/libexec/__init__.py
treeshrink/Tree_extend.py
treeshrink/__init__.py
treeshrink/alignment.py
treeshrink/decompose_lib.py
treeshrink/filemgr.py
treeshrink/filter_lib.py
treeshrink/optimal_filter_lib.py
treeshrink/sequence_lib.py
treeshrink/tree_lib.py
treeshrink/util_lib.py