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.gitignore
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.gitignore
data/
*.vcf
*.fastq
*.gz
*.bam
*.bai
*.bed
*.fasta
*.fa
*.fai
*.catg
*.h5
*.tmp
*.nex
results/2016-11-18/pop1.geno.ld
results/2016-11-18/pop1.interchrom.geno.ld
results/2016-11-18/pop2.geno.ld
results/2016-11-18/pop2.interchrom.geno.ld
results/2016-11-18/population1.txt
results/2016-11-18/population2.txt
results/2016-11-18/populations3to6.txt
results/2016-11-18/snp_indels_q40.vcf.gz.tbi
results/2016-11-24/combined40.vcf.gz.tbi
results/2016-11-24/population1.txt
results/2016-11-24/population2.txt
results/2016-11-30/coverage_matrix.txt
results/2017-05-17/readme.err
results/2017-05-17/readme.log
results/2017-05-18/hhog.json
results/2017-05-18/ipyrad_log.txt
results/2017-05-18/readme.err
results/2017-05-18/readme.log
results/2017-05-18/reference.fasta.amb
results/2017-05-18/reference.fasta.ann
results/2017-05-18/reference.fasta.bwt
results/2017-05-18/reference.fasta.pac
results/2017-05-18/reference.fasta.sa
results/2017-05-18/step2.err
results/2017-05-18/step2.log
results/2017-05-18/step3.err
results/2017-05-18/step3.log
results/2017-05-18/step4.err
results/2017-05-18/step4.log
results/2017-05-18/step5.err
results/2017-05-18/step5.log
results/2017-05-18/step6.err
results/2017-05-18/step6.log
results/2017-05-18/step7.err
results/2017-05-18/step7.log
results/2017-05-18/z.summary.txt
results/2017-05-18/z1
results/2017-05-25/readme.err
results/2017-05-25/readme.log
results/2017-05-18/hhog_consens/hhog-tmpaligns/
results/2017-05-18/hhog_consens/hhog.clust.hdf5
results/2017-05-18/hhog_consens/hhog.htemp
results/2017-05-18/hhog_consens/hhog.tmp.indels
results/2017-05-18/hhog_consens/hhog.utemp
results/2017-05-18/hhog_consens/hhog.utemp.sort
results/2017-05-18/hhog_outfiles/hhog.alleles.loci
results/2017-05-18/hhog_outfiles/hhog.geno
results/2017-05-18/hhog_outfiles/hhog.gphocs
results/2017-05-18/hhog_outfiles/hhog.hdf5
results/2017-05-18/hhog_outfiles/hhog.loci
results/2017-05-18/hhog_outfiles/hhog.phy
results/2017-05-18/hhog_outfiles/hhog.snps.map
results/2017-05-18/hhog_outfiles/hhog.snps.phy
results/2017-05-18/hhog_outfiles/hhog.str
results/2017-05-18/hhog_outfiles/hhog.u.geno
results/2017-05-18/hhog_outfiles/hhog.u.snps.phy
results/2017-05-18/hhog_outfiles/hhog.ustr
results/2017-05-18/ipyrad_log.txt_old
results/2017-05-18/min5.json
results/2017-05-18/min5_outfiles/
results/2017-05-18/vcf.json
results/2017-05-18/vcf.log
results/2017-05-18/vcf_outfiles/
results/2017-06-09/jmodeltest
results/2017-06-09/species_maps
results/2018-03-27/beforeafter.diff.sites_in_files
results/2018-03-27/coverage_matrix.txt
results/2018-04-13/both_across/both.clust.hdf5
results/2018-04-13/both_across/both.utemp.sort
results/2018-04-13/both_outfiles/both.alleles.loci
results/2018-04-13/both_outfiles/both.geno
results/2018-04-13/both_outfiles/both.gphocs
results/2018-04-13/both_outfiles/both.hdf5
results/2018-04-13/both_outfiles/both.loci
results/2018-04-13/both_outfiles/both.phy
results/2018-04-13/both_outfiles/both.snps.map
results/2018-04-13/both_outfiles/both.snps.phy
results/2018-04-13/both_outfiles/both.str
results/2018-04-13/both_outfiles/both.u.geno
results/2018-04-13/both_outfiles/both.u.snps.phy
results/2018-04-13/both_outfiles/both.ustr
results/2018-03-27b/all_min*.tsv
results/2018-06-30/Er*.out
results/2018-06-30/*/NotPlotted.txt
results/2018-06-30/Er37_SK27/NW_00680393*
results/2018-06-30/Er37_SK27/NW_00680394*
results/2018-06-30/Er37_SK27/NW_00680395*
results/2018-06-30/Er37_SK27/NW_00680396*
results/2018-06-30/Er37_SK27/NW_00680397*
results/2018-06-30/Er37_SK27/NW_00680398*
results/2018-06-30/Er37_SK27/NW_00680399*
results/2018-06-30/Er37_SK27/NW_006804*
results/2018-06-30/Er51_436/*
results/2018-06-30/Er53_ASR7/*
results/2018-06-30/Er66_IT3/*
results/2018-06-30/Er30_79/*
results/2018-06-30/Er37_SK27/ENum/NW_00680*
results/2018-06-30/Er37_SK27/LOD/NW_00680*
results/2018-06-30/Er26_JUG4/
results/2018-06-30/Er50_R3/
results/2018-06-30/Er55_AU7/
results/2018-08-01/ConSpectrum.txt
results/2018-08-01/Er26.Q
results/2018-08-01/Er26.profile
results/2018-08-01/EurSpectrum.txt
results/2018-08-01/LOD3.012
results/2018-08-01/LOD3_EmpiricalFreq.txt
results/2018-08-01/LOD3_P.txt
results/2018-08-01/LOD3_ordered.012
results/2018-08-01/LOD3_positions.txt
results/2018-08-01/PopulationNames.txt
results/2018-08-01/RouSpectrum.txt
results/2018-08-01/ancestry_1.txt
results/2018-08-01/ancestry_2.txt
results/2018-08-01/ancestry_3.txt
results/2018-08-01/frequencies.txt
results/2018-10-03/Er26_JUG4/NW*
results/2018-10-03/Er27_SK32/NW*
results/2018-10-03/Er37_SK27/NW*
results/2018-10-03/Er55_AU7/NW*
results/2018-10-08/erinaceus*.Q
results/2018-10-08/out.012.indv
results/2018-10-15/*.tsv
results/2018-10-18/*.tsv
results/2018-10-24/*.tsv
results/2018-10-29/*.tsv
results/2018-12-15/*.012
results/2018-12-15/*.012.pos
results/2018-12-15/*/*.hdf5
results/2018-12-15/*/*chain*.txt
bin/clinEff/*
bin/genomeannotation-GAG-997e384/*
bin/snpEff/*
results/2020-02-12/all_depths.txt
results/2020-02-12/logs
results/2020-02-12/sam
results/2020-04-07/*.geno.gz
results/2020-04-08/erin63.geno.gz
results/2020-04-08/subsampling/*.geno.gz
results/2020-05-06/europaeus_admixed/ea.sel
results/2020-05-06/roumanicus_admixed/ra.sel
results/2020-06-26/europaeus/*.sel
results/2020-06-26/roumanicus/*.sel
results/2020-06-15/fasta/*
results/2020-06-15/.RData
results/2020-09-28/asian/rep*
results/2020-09-28/balkan/rep*
results/2020-09-28/amurensis/rep*
results/2020-09-28/iberian/rep*
results/2020-09-28/apennine/rep*
results/2020-09-28/concolor/rep*
results/2020-09-28/asian_apennine/rep*
results/2020-09-28/asian_apennine/popmap*
results/2020-09-28/asian_iberian/rep*
results/2020-09-28/asian_iberian/popmap*
results/2020-09-28/asian_amurensis/rep*
results/2020-09-28/asian_amurensis/popmap*
results/2020-09-28/balkan_apennine/rep*
results/2020-09-28/balkan_apennine/popmap*
results/2020-09-28/balkan_iberian/rep*
results/2020-09-28/balkan_iberian/popmap*
results/2020-09-28/balkan_amurensis/rep*
results/2020-09-28/balkan_amurensis/popmap*
results/2021-11-17/all.gdepth
results/2021-12-01/*.gdepth
results/2021-12-06/*.saf.gz
results/2021-12-06/*.saf.pos.gz
results/2022-02-08/k/
results/2022-02-08/all_loci/
results/2022-02-08/lowR2/*.hdf5
results/2022-02-08/lowR2/*post.txt