├── ATAC ├── FW_5th_H_erato_normalized_mean.w30s0bin.bg ├── FW_5th_H_erato_normalized_mean.w30s0bin_end.pan.txt ├── FW_5th_H_erato_normalized_mean.w30s0bin_end.txt ├── FW_5th_H_erato_normalized_mean.w30s0bin_start.pan.txt ├── FW_5th_H_erato_normalized_mean.w30s0bin_start.txt ├── FW_5th_H_melp_normalized_mean.w30s0bin.bg ├── README.md ├── brain_5th_H_erato_normalized_mean.w30s0bin.bg ├── brain_5th_H_erato_normalized_mean.w30s0bin_end.pan.txt ├── brain_5th_H_erato_normalized_mean.w30s0bin_end.txt ├── brain_5th_H_erato_normalized_mean.w30s0bin_start.pan.txt ├── brain_5th_H_erato_normalized_mean.w30s0bin_start.txt ├── brain_5th_H_melp_normalized_mean.w30s0bin.bg ├── erato_5th_FW_end.pan.txt ├── erato_5th_FW_end.toMap.txt ├── erato_5th_FW_start.pan.txt ├── erato_5th_FW_start.toMap.txt ├── erato_5th_brain_end.pan.txt ├── erato_5th_brain_end.toMap.txt ├── erato_5th_brain_start.pan.txt ├── erato_5th_brain_start.toMap.txt ├── melp_5th_FW_end.pan.txt ├── melp_5th_FW_end.toMap.txt ├── melp_5th_FW_start.pan.txt ├── melp_5th_FW_start.toMap.txt ├── melp_5th_brain_end.pan.txt ├── melp_5th_brain_end.toMap.txt ├── melp_5th_brain_start.pan.txt └── melp_5th_brain_start.toMap.txt ├── Minimap2_out ├── Minimap_erato_melp.sam ├── Minimap_melp_erato.sam ├── README.md ├── miniMap_query_end.pan.txt ├── miniMap_query_end.toMap.txt ├── miniMap_query_start.pan.txt ├── miniMap_query_start.toMap.txt ├── miniMap_target_end.pan.txt ├── miniMap_target_end.toMap.txt ├── miniMap_target_start.pan.txt └── miniMap_target_start.toMap.txt ├── Plot_minimap_alignment.R ├── Plot_pan_genome.R ├── README.md ├── TEs ├── H_erato_1801_TE.txt ├── H_melp_18003_TE.txt ├── README.md ├── TE_erato_end.pan.txt ├── TE_erato_end.toMap.txt ├── TE_erato_start.pan.txt ├── TE_erato_start.toMap.txt ├── TE_melp_end.pan.txt ├── TE_melp_end.toMap.txt ├── TE_melp_start.pan.txt └── TE_melp_start.toMap.txt ├── gene_annotation ├── README.md ├── optix_Hmel2.toMap.pan.txt └── optix_Hmel2.toMap.txt ├── genome_list.txt ├── seq-seq-pan_bedfile_conservation.py ├── seq-seq-pan_bedgraph_chrompos.py ├── seq-seq-pan_blocks_intervals.py ├── seq-seq-pan_out ├── 1_blocks_intervals.bed ├── 2_blocks_intervals.bed ├── README.md ├── SeqSeqPan_erato_melp_optix.fasta ├── SeqSeqPan_erato_melp_optix.maf ├── SeqSeqPan_erato_melp_optix.noNewline.xmfa ├── SeqSeqPan_erato_melp_optix.xmfa ├── SeqSeqPan_erato_melp_optix_consensus.fasta ├── SeqSeqPan_erato_melp_optix_consensus.fasta.blockseparated.fasta ├── SeqSeqPan_erato_melp_optix_consensus.fasta.blockseparated.idx ├── SeqSeqPan_erato_melp_optix_consensus.fasta.idx ├── SeqSeqPan_erato_melp_optix_genomedescription.txt ├── blocks_shared_1_2.bed ├── blocks_unique_1.bed ├── blocks_unique_2.bed ├── conservation_shared_1_2.bed.txt ├── genome_1.fasta └── genome_2.fasta ├── seq-seq-pan_toFasta.py └── sequences ├── Herato1801_1_2000000.fasta ├── Hmel213003_1_2000000.fasta └── README.md /ATAC/FW_5th_H_erato_normalized_mean.w30s0bin.bg: 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