├── .gitignore ├── LICENSE.txt ├── README.md ├── example ├── Example-windows_plot-for-Haplotypes.R.pdf ├── Hybrid-SA.vcf-chr1.bam ├── Hybrid-SA.vcf-chr1.bam.bai ├── Hybrid-SA.vcf-chr1.fasta ├── Hybrid-SA.vcf-chr1.fasta.fai ├── Hybrid-SA.vcf-chr1.vcf ├── Name_Type_Location_consensus_genomes.tab └── consensus_genomes │ ├── .DS_Store │ ├── Asia1-KRBOOR323.vcf-s-supercont1.1-i-n-n-N-consensus.fasta │ ├── Asia2-CLFT065.vcf-s-supercont1.1-i-n-n-N-consensus.fasta │ ├── CAPE-TF5a1.vcf-s-supercont1.1-i-n-n-N-consensus.fasta │ ├── CH-ACON.vcf-s-supercont1.1-i-n-n-N-consensus.fasta │ └── GPL-JEL423.vcf-s-supercont1.1-i-n-n-N-consensus.fasta ├── haplotypetools ├── resources └── logo.png └── util ├── FASTA_compare_sequences.pl ├── GridController.py ├── GridController.pyc ├── HaplotypeTools.pl ├── Haplotype_FASTA_files_to_compare_to_IRMS_het_sites.pl ├── Haplotype_list_count.pl ├── Haplotype_placer.pl ├── Haplotype_placer_windows.pl ├── Run_cmds_on_grid.py ├── VCF_and_FASTA_to_consensus_FASTA.pl ├── 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