script/allele_rate.sample2xparr.pl
script/conv_epistat_prj2site2pheno.pl
script/cpu_info.pl
script/epistat.pl
script/estimate_fdr.pl
script/estimate_tau.pl
script/fake_sample.pl
script/mk_coevolmtx.pl
script/mk_summary.pl
script/rgb.txt
script/run_epistat.pl
script/run_epistat_batch.pl
script/sample2xparr.pl
script/shuffle_incidence_matrix.R
script/union_epistat_projects.pl
script/utils/add_fdr4pvalues.pl
script/utils/check_xparr.pl
script/utils/join_site_pair_tables.pl
script/utils/mk_xparr.pl
script/utils/xparr_prune_tree.pl
script/stat/aggregate_statistics.pl
script/stat/draw_site_pairs_on_tree.pl
script/stat/figtree.colors
script/stat/fishers_exact_test.R
script/stat/mk_fake_wi_scores.pl
script/stat/mk_table.sh
script/stat/multinomial_test.R
script/stat/multisetIntersect.R
script/stat/site_set2site_pairs_test.pl
script/stat/summ_site_groups_tests.pl
script/stat/summ_site_subset_enrich_tests.pl
script/stat/test.tab
script/stat/test_fe.tab
script/stat/wilcox_test.R
script/stat/xparr_enrich_test.pl
script/stat/xparr_site_groups_test.pl
script/stat/xparr_wilcox_test.pl
script/minvert/cor2pcor.R
script/minvert/psicov.R
script/graph/find_partition.py
script/graph/join_edge_lists.pl
script/graph/louvain_modularity.py
script/graph/mk_graph.pl
script/graph/test_louvain.py
doc/BiRewire-1.pdf
lib/Epistat.pm
lib/IndexedFakeSamplesHeap.pm
lib/ParallelSubstWeights.pm
lib/SitePairInfo.pm
lib/SitePairMatrix.pm
lib/SitePairUtils.pm
lib/SubstPairInfo.pm
lib/AssociationStatistics/BaseAssociationMeasure.pm
lib/AssociationStatistics/basicAssociationFilter.pm
lib/AssociationStatistics/BasicIndexFilter.pm
lib/AssociationStatistics/CorrelationLike.pm
lib/AssociationStatistics/CovarianceLike.pm
lib/AssociationStatistics/NonNegativeValueFilter.pm
lib/AssociationStatistics/NormZScore.pm
lib/AssociationStatistics/PairMutationNumberFilter.pm
lib/AssociationStatistics/PvalueFilter.pm
lib/AssociationStatistics/SelectedSitesFilter.pm
lib/AssociationStatistics/SiteMutationNumberFilter.pm
lib/AssociationStatistics/SymBaseAssociationMeasure.pm
lib/AssociationStatistics/SymCorrelationLike.pm
lib/AssociationStatistics/SymCorrelationLike1.pm
lib/AssociationStatistics/SymCovarianceLike.pm
lib/AssociationStatistics/SymCovarianceLike1.pm
lib/AssociationStatistics/SymIndexFilter.pm
lib/AssociationStatistics/SymNonNegativeValueFilter.pm
lib/AssociationStatistics/SymNormZScore.pm
lib/AssociationStatistics/SymZScore.pm
lib/AssociationStatistics/ZScore.pm
lib/DnaUtilities/compare.pm
lib/DnaUtilities/FASTASimple.pm
lib/DnaUtilities/grouppedMSA.pm
lib/DnaUtilities/iupac.pm
lib/DnaUtilities/CDS/annotation.pm
lib/EpistatAnalysis/PhyloDistances.pm
lib/EpistatAnalysis/PhyloDrawSites.pm
lib/EpistatNullModel/General.pm
lib/EpistatNullModel/Symmetric.pm
lib/IO/EmpiricalMutationModel.pm
lib/IO/SitePairIdxData.pm
lib/IO/XPARR.pm
lib/Pairs/AlleleBranchPairs.pm
lib/Pairs/AlleleConsecutivePairs.pm
lib/Pairs/BranchPairs.pm
lib/Pairs/ConsecutivePairs.pm
lib/Phenotype/AggregateStatistics.pm
lib/SiteModel/AlleleMutRates.pm
lib/SiteModel/EmpiricalProfile.pm
lib/SiteModel/ProteinMixtureModelProfile.pm
lib/TreeUtils/Phylo/FigTree.pm
t/t_install_ok.t
t/data/mixed.block.mtx
t/data/mixed.epistat.prm
t/data/mixed.intra.fgr.idx2branch.1
t/data/mixed.intra.fgr.idx2site.1
t/data/mixed.intra.fgr.mmtx.1
t/data/mixed.mtx
t/data/mixed.sample2xparr.1.prm
t/data/mixed.xparr
t/data/run_epistat.prm
examples/intragene/alleles/cytb/CYTB.einsi.mega.G10.no_gaps.1bgy.pdb_dists
examples/intragene/alleles/cytb/CYTB.einsi.mega.G10.no_gaps.xparr
examples/intragene/alleles/cytb/cytb.epistat.prm
examples/intragene/alleles/cytb/cytb.G10.fas.sitefreq
examples/intragene/alleles/cytb/cytb.lower.pvalue.sites.fdr.prm
examples/intragene/alleles/cytb/cytb.mk_coevolmtx.prm
examples/intragene/alleles/cytb/cytb.mk_summary.cfg
examples/intragene/alleles/cytb/cytb.upper.pvalue.sites.fdr.prm
examples/intragene/alleles/cytb/gnu_parallel.opts
examples/intragene/alleles/cytb/run_epistat.prm
examples/intragene/alleles/sars2_s/cor2pcor.opts
examples/intragene/alleles/sars2_s/run_epistat.prm
examples/intragene/alleles/sars2_s/S.7jjj.pdbdist
examples/intragene/alleles/sars2_s/S.all.mk_coevolmtx.prm
examples/intragene/alleles/sars2_s/S.epistat.prm
examples/intragene/alleles/sars2_s/S.lower.pvalue.unord_pairs.sites.fdr.prm
examples/intragene/alleles/sars2_s/S.lp0052.FDR10.mk_summary.cfg
examples/intragene/alleles/sars2_s/S.mk_coevolmtx.prm
examples/intragene/alleles/sars2_s/S.up00044.FDR10.mk_summary.cfg
examples/intragene/alleles/sars2_s/S.upper.pvalue.unord_pairs.pairs.fdr.prm
examples/intragene/alleles/sars2_s/S.upper.pvalue.unord_pairs.sites.fdr.prm
examples/intragene/alleles/sars2_s/S.xparr
examples/intragene/no_alleles/sars2_s/cor2pcor.opts
examples/intragene/no_alleles/sars2_s/run_epistat.prm
examples/intragene/no_alleles/sars2_s/S.all.mk_coevolmtx.prm
examples/intragene/no_alleles/sars2_s/S.epistat.prm
examples/intragene/no_alleles/sars2_s/S.lower.pvalue.unord_pairs.sites.fdr.prm
examples/intragene/no_alleles/sars2_s/S.lp0052.FDR10.mk_summary.cfg
examples/intragene/no_alleles/sars2_s/S.mk_coevolmtx.prm
examples/intragene/no_alleles/sars2_s/S.up00044.FDR10.mk_summary.cfg
examples/intragene/no_alleles/sars2_s/S.upper.pvalue.unord_pairs.pairs.fdr.prm
examples/intragene/no_alleles/sars2_s/S.upper.pvalue.unord_pairs.sites.fdr.prm
examples/intragene/no_alleles/sars2_s/S.xparr
script_graph_list.txt
script_minvert_list.txt
script_stat_list.txt
script_utils_list.txt
examples_list.txt
Build.PL
MANIFEST			This list of files