Name		Name	Last commit message	Last commit date
deprecated		deprecated
BTB_get_taxid_from_gi.py		BTB_get_taxid_from_gi.py
ChoosePopLDinfile.py		ChoosePopLDinfile.py
NONAtsv2txt.sh		NONAtsv2txt.sh
Q10.sh		Q10.sh
Q30.sh		Q30.sh
Q30AC1.sh		Q30AC1.sh
README.md		README.md
Rbatch.sh		Rbatch.sh
abyss-fac.pl		abyss-fac.pl
admixture.sh		admixture.sh
admixture.sh.save		admixture.sh.save
angsd_idx_to_fst.sh		angsd_idx_to_fst.sh
aseQ10.sh		aseQ10.sh
balancetest.sh		balancetest.sh
bamToFastq.sh		bamToFastq.sh
bam_counts.sh		bam_counts.sh
batch-blast-ncbiprot.sh		batch-blast-ncbiprot.sh
batch-blast-nr.sh		batch-blast-nr.sh
batch-blast-uniprot.sh		batch-blast-uniprot.sh
batch-bowtie2-bam-single.sh		batch-bowtie2-bam-single.sh
batch-bowtie2-fq-flash.sh		batch-bowtie2-fq-flash.sh
batch-bowtie2-fq-paired-local.sh		batch-bowtie2-fq-paired-local.sh
batch-bowtie2-fq-paired-nodedup.sh		batch-bowtie2-fq-paired-nodedup.sh
batch-bowtie2-fq-paired-strict.sh		batch-bowtie2-fq-paired-strict.sh
batch-bowtie2-fq-paired-unfiltered.sh		batch-bowtie2-fq-paired-unfiltered.sh
batch-bowtie2-fq-paired-vsallqual.sh		batch-bowtie2-fq-paired-vsallqual.sh
batch-bowtie2-fq-paired.sh		batch-bowtie2-fq-paired.sh
batch-bowtie2-fq-single-dedup.sh		batch-bowtie2-fq-single-dedup.sh
batch-bowtie2-fq-single-vsl.sh		batch-bowtie2-fq-single-vsl.sh
batch-bowtie2-fq-single.sh		batch-bowtie2-fq-single.sh
batch-deduplicateSE.sh		batch-deduplicateSE.sh
batch-fastqc.sh		batch-fastqc.sh
batch-fastx-qualstats.sh		batch-fastx-qualstats.sh
batch-filter-assembly.sh		batch-filter-assembly.sh
batch-flash.sh		batch-flash.sh
batch-hisat2-fq-paired-eas.sh		batch-hisat2-fq-paired-eas.sh
batch-hisat2-fq-paired.sh		batch-hisat2-fq-paired.sh
batch-hisat2-fq-single.sh		batch-hisat2-fq-single.sh
batch-hisat2-fq-single_dedup.sh		batch-hisat2-fq-single_dedup.sh
batch-parse-nr.sh		batch-parse-nr.sh
batch-parse-uniprot.sh		batch-parse-uniprot.sh
batch-rgs.sh		batch-rgs.sh
batch-sort-index.sh		batch-sort-index.sh
batch-subset-bam.sh		batch-subset-bam.sh
batch-taxonID-from-gi.sh		batch-taxonID-from-gi.sh
batch-template.sh		batch-template.sh
batch-trimmomatic-nextera.sh		batch-trimmomatic-nextera.sh
batch-trimmomatic-pe.sh		batch-trimmomatic-pe.sh
batch-trimmomatic-se.sh		batch-trimmomatic-se.sh
batch-wasp.sh		batch-wasp.sh
bayescan.sh		bayescan.sh
bcftools_filter.sh		bcftools_filter.sh
bcftools_parallel.sh		bcftools_parallel.sh
bcftools_parallel_eas.sh		bcftools_parallel_eas.sh
bed2gffCDS.sh		bed2gffCDS.sh
bed_bams_coverage.sh		bed_bams_coverage.sh
bedfile_linkage.sh		bedfile_linkage.sh
bedfile_linkage_dummy.sh		bedfile_linkage_dummy.sh
bedfile_linkage_maxd.sh		bedfile_linkage_maxd.sh
blast2gffCDS.sh		blast2gffCDS.sh
blastx-ncbiprotein.sh		blastx-ncbiprotein.sh
blastx-nr.sh		blastx-nr.sh
blastx-uniprot.sh		blastx-uniprot.sh
blat.sh		blat.sh
cap3.sh		cap3.sh
combine_cds.py		combine_cds.py
dummy_chrom.py		dummy_chrom.py
example-CAP3-mkm.sh		example-CAP3-mkm.sh
example_FLASH_mkm.sh		example_FLASH_mkm.sh
example_Trimmomatic_MKM.sbatch		example_Trimmomatic_MKM.sbatch
example_Trinity_mkm.sbatch		example_Trinity_mkm.sbatch
example_fastqc_MKM.sh		example_fastqc_MKM.sh
example_tBLASTx_localdb_customout_mkm.sbatch		example_tBLASTx_localdb_customout_mkm.sbatch
expr-divergence.R		expr-divergence.R
extract_exons.py		extract_exons.py
extract_impute_snps.sh		extract_impute_snps.sh
extract_splice_sites.py		extract_splice_sites.py
extract_vcf_snps.sh		extract_vcf_snps.sh
fastVCFcombine.sh		fastVCFcombine.sh
fasta2bed.sh		fasta2bed.sh
fastxQC.sh		fastxQC.sh
filter-assembly.py		filter-assembly.py
filterEff.sh		filterEff.sh
filter_fasta_by_length.sh		filter_fasta_by_length.sh
filter_remapped_reads.py		filter_remapped_reads.py
find_intersecting_snps.py		find_intersecting_snps.py
fix-weird-freebayes-snps.py		fix-weird-freebayes-snps.py
fix_freebayes_snps.py		fix_freebayes_snps.py
freebayes-cluster.sh		freebayes-cluster.sh
freebayes-filter-hets.sh		freebayes-filter-hets.sh
freebayes-filter.sh		freebayes-filter.sh
freebayes-sequential-intervals.sbatch		freebayes-sequential-intervals.sbatch
freebayes-sequential.sbatch		freebayes-sequential.sbatch
freebayes_nodes.sh		freebayes_nodes.sh
gdriveupload.sh		gdriveupload.sh
generate-WASP-snps.sh		generate-WASP-snps.sh
genolike.arg		genolike.arg
get-bam-counts.sh		get-bam-counts.sh
get-bam-snps.sh		get-bam-snps.sh