├── README.md ├── bin ├── make_pan.pl └── ppsPCP.sh ├── example ├── Zjn_sc00188.1.fa ├── Zjn_sc00188.1.gff3 ├── Zmw_sc00394.1.fa ├── Zmw_sc00394.1.gff3 ├── pangenome1.fa ├── pangenome1.gff3 ├── run.log └── tmp │ ├── Zjn_sc00188.1.2.bed │ ├── Zjn_sc00188.1.3.bed │ ├── Zjn_sc00188.1.bed │ ├── Zjn_sc00188.1.fa │ ├── Zjn_sc00188.1.fa.fai │ ├── Zjn_sc00188.1.gff3 │ ├── Zjn_sc00188.1_absence.fa │ ├── Zjn_sc00188.1_absence.txt │ ├── Zjn_sc00188.1_absence_filtered.fa │ ├── Zjn_sc00188.1_absence_pavs.txt │ ├── Zjn_sc00188.1_all.gene.list.txt │ ├── Zjn_sc00188.1_draft.bed │ ├── Zjn_sc00188.1_exons.fa │ ├── Zjn_sc00188.1_exons_longest.fa │ ├── Zjn_sc00188.1_final.bed │ ├── Zjn_sc00188.1_gene_relocation.gff3 │ ├── Zjn_sc00188.1_gene_relocation.txt │ ├── Zjn_sc00188.1_gene_relocation_final.gff3 │ ├── Zjn_sc00188.1_gene_relocation_final.txt │ ├── Zjn_sc00188.1_loci.gff3 │ ├── Zjn_sc00188.1_mapped.gene.list.txt │ ├── Zjn_sc00188.1_pav.agp │ ├── Zjn_sc00188.1_pav.bed │ ├── Zjn_sc00188.1_pav_final.agp │ ├── Zjn_sc00188.1_pav_final.bed │ ├── Zjn_sc00188.1_pav_final.fa │ ├── Zjn_sc00188.1_pav_intersect_gene.gff3 │ ├── Zjn_sc00188.1_pav_intersect_gene_final.gff3 │ ├── Zjn_sc00188.1_pav_region.txt │ ├── Zjn_sc00188.1_pav_region_final.txt │ ├── Zjn_sc00188.1_pav_region_final2.txt │ ├── Zjn_sc00188.1_pav_region_final3.txt │ ├── Zjn_sc00188.1_pav_seq.fa │ ├── Zjn_sc00188.1_pav_seq_final.fa │ ├── Zjn_sc00188.1_pavs_confirm_final.fa │ ├── Zjn_sc00188.1_pavs_confirm_final2.fa │ ├── Zjn_sc00188.1_unmapped.genes.txt │ ├── Zjn_sc00188.1_unmapped_pavs.txt │ ├── Zjn_sc00188.1toZmw_sc00394.1.delta │ ├── Zjn_sc00188.1toZmw_sc00394.1.rq.coords │ ├── Zjn_sc00188.1toZmw_sc00394.1.rq.delta │ ├── Zjn_sc00188.1toZmw_sc00394.1_blastn.txt │ ├── Zjn_sc00188.1toZmw_sc00394.1_draft_genome.fa │ ├── Zjn_sc00188.1toZmw_sc00394.1_output.psl │ ├── Zmw_sc00394.1.fa │ ├── Zmw_sc00394.1.gff3 │ ├── Zmw_sc00394.1_absence.txt │ ├── Zmw_sc00394.1_database.nhr │ ├── Zmw_sc00394.1_database.nin │ ├── 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