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.gitignore
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create_hgt_pool
evolve
examples/test_6/dmm
examples/test_6/example.family_presence
examples/test_6/example.gene_families
examples/test_6/example.gene_parents
examples/test_6/example.genes
examples/test_6/example.genome_sequences
examples/test_6/example.pan_distribution
examples/test_6/cv/genome_0.ffn.cv5.gz
examples/test_6/cv/genome_0.ffn.cv6.gz
examples/test_6/cv/genome_0.ffn.cv7.gz
examples/test_6/cv/genome_1.ffn.cv5.gz
examples/test_6/cv/genome_1.ffn.cv6.gz
examples/test_6/cv/genome_1.ffn.cv7.gz
examples/test_6/cv/genome_2.ffn.cv5.gz
examples/test_6/cv/genome_2.ffn.cv6.gz
examples/test_6/cv/genome_2.ffn.cv7.gz
examples/test_6/cv/genome_3.ffn.cv5.gz
examples/test_6/cv/genome_3.ffn.cv6.gz
examples/test_6/cv/genome_3.ffn.cv7.gz
examples/test_6/cv/genome_4.ffn.cv5.gz
examples/test_6/cv/genome_4.ffn.cv6.gz
examples/test_6/cv/genome_4.ffn.cv7.gz
examples/test_6/cv/genome_5.ffn.cv5.gz
examples/test_6/cv/genome_5.ffn.cv6.gz
examples/test_6/cv/genome_5.ffn.cv7.gz
examples/test_6/cv/genome_6.ffn.cv5.gz
examples/test_6/cv/genome_6.ffn.cv6.gz
examples/test_6/cv/genome_6.ffn.cv7.gz
examples/test_6/cv/genome_7.ffn.cv5.gz
examples/test_6/cv/genome_7.ffn.cv6.gz
examples/test_6/cv/genome_7.ffn.cv7.gz
examples/test_6/cv/genome_8.ffn.cv5.gz
examples/test_6/cv/genome_8.ffn.cv6.gz
examples/test_6/cv/genome_8.ffn.cv7.gz
examples/test_6/cv/genome_9.ffn.cv5.gz
examples/test_6/cv/genome_9.ffn.cv6.gz
examples/test_6/cv/genome_9.ffn.cv7.gz
examples/test_6/cv/genome_10.ffn.cv5.gz
examples/test_6/cv/genome_10.ffn.cv6.gz
examples/test_6/cv/genome_10.ffn.cv7.gz
examples/test_6/cv/genome_11.ffn.cv5.gz
examples/test_6/cv/genome_11.ffn.cv6.gz
examples/test_6/cv/genome_11.ffn.cv7.gz
examples/test_6/cv/genome_12.ffn.cv5.gz
examples/test_6/cv/genome_12.ffn.cv6.gz
examples/test_6/cv/genome_12.ffn.cv7.gz
examples/test_6/cv/genome_13.ffn.cv5.gz
examples/test_6/cv/genome_13.ffn.cv6.gz
examples/test_6/cv/genome_13.ffn.cv7.gz
examples/test_6/cv/genome_14.ffn.cv5.gz
examples/test_6/cv/genome_14.ffn.cv6.gz
examples/test_6/cv/genome_14.ffn.cv7.gz
examples/test_6/cv/genome_15.ffn.cv5.gz
examples/test_6/cv/genome_15.ffn.cv6.gz
examples/test_6/cv/genome_15.ffn.cv7.gz
examples/test_6/cv/genome_16.ffn.cv5.gz
examples/test_6/cv/genome_16.ffn.cv6.gz
examples/test_6/cv/genome_16.ffn.cv7.gz
examples/test_6/cv/genome_17.ffn.cv5.gz
examples/test_6/cv/genome_17.ffn.cv6.gz
examples/test_6/cv/genome_17.ffn.cv7.gz
examples/test_6/cv/genome_18.ffn.cv5.gz
examples/test_6/cv/genome_18.ffn.cv6.gz
examples/test_6/cv/genome_18.ffn.cv7.gz
examples/test_6/cv/genome_19.ffn.cv5.gz
examples/test_6/cv/genome_19.ffn.cv6.gz
examples/test_6/cv/genome_19.ffn.cv7.gz
examples/test_6/dm/Hao.ffn.cv5.txt
examples/test_6/dm/Hao.ffn.cv6.txt
examples/test_6/dm/Hao.ffn.cv7.txt
examples/test_6/example/ogenomes/genome_0.fna
examples/test_6/example/ogenomes/genome_0.gbff
examples/test_6/example/ogenomes/genome_0.gff
examples/test_6/example/ogenomes/genome_1.fna
examples/test_6/example/ogenomes/genome_1.gbff
examples/test_6/example/ogenomes/genome_1.gff
examples/test_6/example/ogenomes/genome_2.fna
examples/test_6/example/ogenomes/genome_2.gbff
examples/test_6/example/ogenomes/genome_2.gff
examples/test_6/example/ogenomes/genome_3.fna
examples/test_6/example/ogenomes/genome_3.gbff
examples/test_6/example/ogenomes/genome_3.gff
examples/test_6/example/ogenomes/genome_4.fna
examples/test_6/example/ogenomes/genome_4.gbff
examples/test_6/example/ogenomes/genome_4.gff
examples/test_6/example/ogenomes/genome_5.fna
examples/test_6/example/ogenomes/genome_5.gbff
examples/test_6/example/ogenomes/genome_5.gff
examples/test_6/example/ogenomes/genome_6.fna
examples/test_6/example/ogenomes/genome_6.gbff
examples/test_6/example/ogenomes/genome_6.gff
examples/test_6/example/ogenomes/genome_7.fna
examples/test_6/example/ogenomes/genome_7.gbff
examples/test_6/example/ogenomes/genome_7.gff
examples/test_6/example/ogenomes/genome_8.fna
examples/test_6/example/ogenomes/genome_8.gbff
examples/test_6/example/ogenomes/genome_8.gff
examples/test_6/example/ogenomes/genome_9.fna
examples/test_6/example/ogenomes/genome_9.gbff
examples/test_6/example/ogenomes/genome_9.gff
examples/test_6/example/ogenomes/genome_10.fna
examples/test_6/example/ogenomes/genome_10.gbff
examples/test_6/example/ogenomes/genome_10.gff
examples/test_6/example/ogenomes/genome_11.fna
examples/test_6/example/ogenomes/genome_11.gbff
examples/test_6/example/ogenomes/genome_11.gff
examples/test_6/example/ogenomes/genome_12.fna
examples/test_6/example/ogenomes/genome_12.gbff
examples/test_6/example/ogenomes/genome_12.gff
examples/test_6/example/ogenomes/genome_13.fna
examples/test_6/example/ogenomes/genome_13.gbff
examples/test_6/example/ogenomes/genome_13.gff
examples/test_6/example/ogenomes/genome_14.fna
examples/test_6/example/ogenomes/genome_14.gbff
examples/test_6/example/ogenomes/genome_14.gff
examples/test_6/example/ogenomes/genome_15.fna
examples/test_6/example/ogenomes/genome_15.gbff
examples/test_6/example/ogenomes/genome_15.gff
examples/test_6/example/ogenomes/genome_16.fna
examples/test_6/example/ogenomes/genome_16.gbff
examples/test_6/example/ogenomes/genome_16.gff
examples/test_6/example/ogenomes/genome_17.fna
examples/test_6/example/ogenomes/genome_17.gbff
examples/test_6/example/ogenomes/genome_17.gff
examples/test_6/example/ogenomes/genome_18.fna
examples/test_6/example/ogenomes/genome_18.gbff
examples/test_6/example/ogenomes/genome_18.gff
examples/test_6/example/ogenomes/genome_19.fna
examples/test_6/example/ogenomes/genome_19.gbff
examples/test_6/example/ogenomes/genome_19.gff
examples/test_6/gg/genome_0.ffn
examples/test_6/gg/genome_1.ffn
examples/test_6/gg/genome_2.ffn
examples/test_6/gg/genome_3.ffn
examples/test_6/gg/genome_4.ffn
examples/test_6/gg/genome_5.ffn
examples/test_6/gg/genome_6.ffn
examples/test_6/gg/genome_7.ffn
examples/test_6/gg/genome_8.ffn
examples/test_6/gg/genome_9.ffn
examples/test_6/gg/genome_10.ffn
examples/test_6/gg/genome_11.ffn
examples/test_6/gg/genome_12.ffn
examples/test_6/gg/genome_13.ffn
examples/test_6/gg/genome_14.ffn
examples/test_6/gg/genome_15.ffn
examples/test_6/gg/genome_16.ffn
examples/test_6/gg/genome_17.ffn
examples/test_6/gg/genome_18.ffn
examples/test_6/gg/genome_19.ffn
examples/test_6/tree/Hao.ffn.cv5.nwk
examples/test_6/tree/Hao.ffn.cv6.nwk
examples/test_6/tree/Hao.ffn.cv7.nwk
examples/test_6/gglist