├── DESCRIPTION ├── MD5 ├── NAMESPACE ├── NEWS ├── R ├── APE_read.nexus.data.R ├── APE_write.dna.R ├── BAYESRETURN.R ├── DATA.R ├── D_jacknife.R ├── DsDn.R ├── DsPsDnPn.R ├── Ewens_Watt.R ├── GEN.R ├── GENOME.R ├── GFF_split_into_scaffolds.R ├── LOAD.R ├── MK.R ├── MS.R ├── MS_getStats.R ├── MS_jointfreqdist.R ├── PG_plot.biallelic.matrix.R ├── PopGenread.R ├── PopGplot.R ├── PsPn.R ├── SNPFST.R ├── VCF_split_into_scaffolds.R ├── Whop_readVCF.R ├── Yach.stats.R ├── calc.R2.R ├── calc.fixed.shared.R ├── calcR2.R ├── calc_BD.R ├── calc_Bd_CLR_table.R ├── calc_Bd_clr.R ├── calc_D.R ├── calc_FS.R ├── calc_RNDmin.R ├── calc_df.R ├── calc_diversities.R ├── calc_freqstats.R ├── calc_freqstats_FAST.R ├── calc_hwhafsth.R ├── calc_hwhafsth_FAST.R ├── calc_miss.R ├── calc_phi_st.R ├── calc_sxsfss.R ├── check_init_length.R ├── checkpoppairs.R ├── coalsim.R ├── codonise64.R ├── codontable.R ├── complike.R ├── compute_intern_achaz.R ├── concatenate.R ├── concatenate.classes.R ├── concatenate.regions.R ├── count.unknowns.R ├── counthaplotype.R ├── create.PopGenome.method.R ├── csstatsClass.R ├── decodonise64.R ├── delNULLpop.R ├── deletecodongaps.R ├── diversity.stats.R ├── diversity.stats.between.R ├── ehh.R ├── fisherextest.R ├── fitting_gff.R ├── freqtest_achaz.R ├── fstcalc.R ├── genetree.R ├── get.biallelic.matrix.R ├── get.codons.R ├── get.feature.names.R ├── get.individuals.R ├── get.recomb.R ├── get.sweeps.R ├── getTable.R ├── get_data.R ├── get_fixed_shared.R ├── get_gff_info.R ├── get_segsites.R ├── getsyn.R ├── getsynnonsyndiff.R ├── gtest.R ├── haplochi2.r ├── hudsonkaplan85rm.R ├── import_export_slim.R ├── init_coef.R ├── intern.calc.R2.R ├── introgression.stats.R ├── jack.knife.transform.R ├── jointfreqdist.R ├── jump.window.transform.R ├── linkdisequ.R ├── linkdisequ_FAST.R ├── locstatsClass.R ├── mismatch.R ├── mktest.R ├── mult.linkage.stats.R ├── myReadVCF.R ├── my_math.R ├── my_rdirichlet.R ├── my_read.nexus.R ├── my_unique.R ├── neuttest.R ├── pair_linkdisequ.R ├── pair_linkdisequ_FAST.R ├── parse_HapMap.R ├── parse_gff.R ├── permute.R ├── plot_cs.R ├── polymorph.R ├── popgen.R ├── probabilities.R ├── progress.R ├── read.big.fasta.R ├── read.big.ms.output.R ├── read.ms.output.R ├── readData.R ├── readHapMap.R ├── readMS.R ├── readSNP.R ├── readVCF.R ├── readVCFchunk.R ├── readVCFchunkHap.R ├── recomb.stats.R ├── region.as.fasta.R ├── save_load_GENOME.R ├── set.filter.R ├── set.outgroup.R ├── set.ref.positions.R ├── set.synnonsyn.R ├── set_gff_info.R ├── site_FST.R ├── site_diversity_between.R ├── slide.snp.sep.R ├── sliding.window.transform.fast.R ├── sliding.window.transform.new.R ├── slidingWindow.R ├── slim.R ├── snn.R ├── sortmatrix.R ├── split.GFF.R ├── split_data_into_GFF_attributes.R ├── split_data_into_GFF_features.R ├── splitting.data.R ├── splitting.data.sep.R ├── sweeps.stats.R ├── testparamsClass.R ├── tn93.R ├── update_slim.R ├── wall99bq.R ├── weighted.jackknife.R └── zzz.R ├── data ├── fasta_file.txt.gz ├── gff_file.txt.gz ├── snp_file.txt.gz └── vcf_file.txt.gz ├── inst ├── CITATION ├── COPYRIGHTS └── doc │ ├── An_introduction_to_the_PopGenome_package.Rnw │ ├── An_introduction_to_the_PopGenome_package.pdf │ ├── Integration_of_new_Methods.Rnw │ ├── Integration_of_new_Methods.pdf │ ├── Whole_genome_analyses_using_VCF_files.Rnw │ └── Whole_genome_analyses_using_VCF_files.pdf ├── man ├── Achaz.stats.Rd ├── BayeScanR.Rd ├── F_ST.stats-methods.Rd ├── F_ST.stats.2-methods.Rd ├── GENOME-class.Rd ├── GFF_split_into_scaffolds.Rd ├── MKT-methods.Rd ├── MS.Rd ├── MS_getStats.Rd ├── PG_plot.biallelic.matrix.Rd ├── PopGenome.Rd ├── PopGplot.Rd ├── VCF_split_into_scaffolds.Rd ├── Whop_readVCF.Rd ├── calc.R2-methods.Rd ├── calc.fixed.shared-methods.Rd ├── codontable.Rd ├── concatenate.classes.Rd ├── concatenate.regions.Rd ├── count.unknowns-methods.Rd ├── create.PopGenome.method.Rd ├── detail.stats-methods.Rd ├── diversity.stats-methods.Rd ├── diversity.stats.between-methods.Rd ├── fasta_file.Rd ├── get.biallelic.matrix-methods.Rd ├── get.codons-methods.Rd ├── get.feature.names.Rd ├── get.individuals-methods.Rd ├── get.status-methods.Rd ├── getBayes-methods.Rd ├── get_gff_info.Rd ├── gff_file.Rd ├── introgression.stats.Rd ├── jack.knife.transform-methods.Rd ├── linkage.stats-methods.Rd ├── load.session.Rd ├── mult.linkage.stats.Rd ├── neutrality.stats-methods.Rd ├── read.big.fasta.Rd ├── readData.Rd ├── readHapMap.Rd ├── readMS.Rd ├── readSNP.Rd ├── readVCF.Rd ├── recomb.stats-methods.Rd ├── region.as.fasta.Rd ├── save.session.Rd ├── set.filter-methods.Rd ├── set.outgroup-methods.Rd ├── set.populations-methods.Rd ├── set.ref.positions.Rd ├── set.synnonsyn-methods.Rd ├── show.slots-methods.Rd ├── sliding.window.transform-methods.Rd ├── snp_file.Rd ├── split_data_into_GFF_attributes.Rd ├── split_data_into_GFF_features.Rd ├── splitting.data-methods.Rd ├── sweeps.stats-methods.Rd ├── test.params-class.Rd ├── vcf_file.Rd └── weighted.jackknife.Rd ├── src ├── C_get_sfreqh_C.c ├── CompareVEK.c ├── Makevars ├── Makevars.win ├── PopGenome-win.def ├── R2_C.c ├── VCF_split.cpp ├── ap_pop_C.c ├── ap_pop_ancestral_C.c ├── code_nucs.c ├── combnsum2_C.c ├── combnsum_C.c ├── compute_FREQOUT_C.c ├── compute_FREQ_C.c ├── dummy.cc ├── filldiplomatrix.c ├── find_lines.c ├── find_windowC.c ├── fittingGFFC++.c ├── get_dim_fasta.c ├── get_gff_info_C.c ├── get_ind_fasta.c ├── get_segsites_C.c ├── init.c ├── makeBial.c ├── makeBialMatrix.c ├── myReadVCFC.c ├── my_match_C.c ├── my_unique_C.c ├── tabix │ ├── bam_endian.h │ ├── bedidx.c │ ├── bgzf.c │ ├── bgzf.h │ ├── bgzf_bak.c │ ├── bgzf_bak.h │ ├── index.c │ ├── khash.h │ ├── knetfile.c │ ├── knetfile.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.c │ ├── kstring.h │ └── tabix.h ├── verify_ancestral_C.c └── whopgenome │ ├── dynstorage.h │ ├── rdnapp_Fasta.h │ ├── rdnapp_MAF.h │ ├── rdnapp_MEGA.h │ ├── rdnapp_Phylip.h │ ├── readdnapp.cpp │ ├── whop_r_dataframe.cpp │ ├── whop_rsupport.h │ ├── whop_tabix.h │ ├── whop_tabix_internal.h │ ├── whop_tools.h │ ├── whop_vcf.h │ ├── whopgen_codemat.cpp │ ├── whopgen_common.h │ ├── whopgen_filtering.cpp │ ├── whopgen_main.cpp │ ├── whopgen_read.cpp │ ├── whopgen_region.cpp │ ├── whopgen_rsupport.cpp │ ├── whopgen_samples.cpp │ ├── whopgen_tools.cpp │ ├── whopgen_vcf.cpp │ ├── whoptbi_Rifc.cpp │ ├── whoptbi_info.cpp │ ├── whoptbi_main.cpp │ ├── whoptbi_read.cpp │ └── whoptbi_region.cpp └── vignettes ├── 2Lslide.pdf ├── An_introduction_to_the_PopGenome_package.Rnw ├── GenesTaj.pdf ├── Integration_of_new_Methods.Rnw ├── PopGenomeClasses.pdf ├── SFS.pdf ├── Whole_genome_analyses_using_VCF_files.Rnw ├── XXX.pdf ├── XYZ.pdf ├── nucFST.pdf └── nucFSTvsAll.pdf /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cran/PopGenome/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /MD5: -------------------------------------------------------------------------------- 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