datadir File List

• README.txt
• RPS_representative.fasta
• RPS_representative.fasta.interpro
• ortholog_exon_intron_sequences.tgz
• proteins_used_for_OrthoFinder.tgz
• strain_list.txt
• strain_metadata.tsv
• GFF/
• GCA_000269785.2.gff
• GCA_000278405.1.gff
• GCA_000278425.1.gff
• GCA_000320905.1.gff
• GCA_000691885.1.gff
• GCA_000952835.1.gff
• GCA_000956085.1.gff
• GCA_001576635.1.gff
• GCA_001576645.1.gff
• GCA_001576655.1.gff
• GCA_001576715.1.gff
• GCA_001576725.1.gff
• GCA_001576735.1.gff
• GCA_001576745.1.gff
• GCA_001576795.1.gff
• GCA_001695535.1.gff
• GCA_002007945.1.gff
• GCA_002214955.1.gff
• GCA_002214965.1.gff
• GCA_002217615.1.gff
• GCA_002217635.1.gff
• GCA_002443195.2.gff
• GCA_002443215.2.gff
• GCA_002456175.2.gff
• GCA_002864195.1.gff
• GCA_002894705.1.gff
• GCA_003709025.1.gff
• GCA_003711285.1.gff
• GCA_003711305.1.gff
• GCA_003711315.1.gff
• GCA_003711345.1.gff
• GCA_003711355.1.gff
• GCA_003711385.1.gff
• GCA_003953485.1.gff
• GCA_003953495.1.gff
• GCA_003953505.1.gff
• GCA_003953515.1.gff
• GCA_003953525.1.gff
• GCA_003953585.1.gff
• GCA_003953595.1.gff
• GCA_003953605.1.gff
• GCA_003953615.1.gff
• GCA_003953625.1.gff
• GCA_003953685.1.gff
• GCA_003953695.1.gff
• GCA_003953705.1.gff
• GCA_003953715.1.gff
• GCA_003953735.1.gff
• GCA_003953785.1.gff
• GCA_003953795.1.gff
• GCA_003953805.1.gff
• GCA_003953825.1.gff
• GCA_003953865.1.gff
• GCA_003967615.1.gff
• GCA_003967635.1.gff
• GCA_003967655.1.gff
• GCA_003967675.1.gff
• GCA_003967695.1.gff
• GCA_003967715.1.gff
• GCA_003967735.1.gff
• GCA_003967755.1.gff
• GCA_003967775.1.gff
• GCA_003967795.1.gff
• GCA_004329145.1.gff
• GCA_004353305.1.gff
• GCF_000006275.2.gff
• GCF_000184455.2.gff
• run1_AD001_ATCACG.gff
• run1_AD002_CGATGT.gff
• run1_AD003_TTAGGC.gff
• run1_AD004_TGACCA.gff
• run1_AD005_ACAGTG.gff
• run1_AD006_GCCAAT.gff
• run1_AD007_CAGATC.gff
• run1_AD008_ACTTGA.gff
• run1_AD012_CTTGTA.gff
• run1_AD013_AGTCAA.gff
• run1_AD014_AGTTCC.gff
• run2_AD002_CGATGT.gff
• run2_AD004_TGACCA.gff
• run2_AD005_ACAGTG.gff
• run2_AD006_GCCAAT.gff
• run2_AD007_CAGATC.gff
• run2_AD010_TAGCTT.gff
• run2_AD011_GGCTAC.gff
• run2_AD012_CTTGTA.gff
• run2_AD013_AGTCAA.gff
• run2_AD014_AGTTCC.gff
• run2_AD015_ATGTCA.gff
• run2_AD016_CCGTCC.gff
• run2_AD018_GTCCGC.gff
• run2_AD019_GTGAAA.gff
• run2_AD020_GTGGCC.gff
• run2_AD021_GTTTCG.gff
• run2_AD022_CGTACG.gff
• run2_AD023_GAGTGG.gff
• run2_AD025_ACTGAT.gff
• run2_AD027_ATTCCT.gff
• run3_index05_ACAGTG.gff
• run3_index06_GCCAAT.gff
• run3_index07_CAGATC.gff
• run3_index08_ACTTGA.gff
• run3_index09_GATCAG.gff
• run3_index10_TAGCTT.gff
• run3_index11_GGCTAC.gff
• run3_index12_CTTGTA.gff
• run3_index13_AGTCAA.gff
• run3_index14_AGTTCC.gff
• run3_index15_ATGTCA.gff
• run3_index16_CCGTCC.gff
• run3_index18_GTCCGC.gff
• run3_index19_GTGAAA.gff
• run3_index20_GTGGCC.gff
• run3_index21_GTTTCG.gff
• run3_index22_CGTACG.gff
• run3_index23_GAGTGG.gff
• run3_index25_ACTGAT.gff
• run3_index27_ATTCCT.gff
• run4_index01_ATCACG.gff
• run4_index02_CGATGT.gff
• run4_index03_TTAGGC.gff
• run4_index04_TGACCA.gff
• run4_index05_ACAGTG.gff
• run4_index06_GCCAAT.gff
• run4_index08_ACTTGA.gff
• run4_index09_GATCAG.gff
• run4_index10_TAGCTT.gff
• run4_index12_CTTGTA.gff
• run4_index13_AGTCAA.gff
• run4_index14_AGTTCC.gff
• run4_index15_ATGTCA.gff
• run4_index18_GTCCGC.gff
• run4_index19_GTGAAA.gff
• run5_index01_ATCACGAT.gff
• run5_index02_CGATGTAT.gff
• run5_index03_TTAGGCAT.gff
• run5_index04_TGACCAAT.gff
• run5_index05_ACAGTGAT.gff
• run5_index06_GCCAATAT.gff
• run5_index07_CAGATCAT.gff
• run5_index08_ACTTGAAT.gff
• run5_index09_GATCAGAT.gff
• run5_index10_TAGCTTAT.gff
• run5_index11_GGCTACAT.gff
• run5_index12_CTTGTAAT.gff
• run5_index13_AGTCAACA.gff
• run5_index14_AGTTCCGT.gff
• run5_index15_ATGTCAGA.gff
• run5_index16_CCGTCCCG.gff
• run5_index20_GTGGCCTT.gff
• run5_index21_GTTTCGGA.gff
• run5_index27_ATTCCTTT.gff
• OrthoFinder_Results/
• Orthogroups.csv
• Orthogroups.csv.BUSCO96.csv
• Orthogroups_UnassignedGenes.csv
• scaffolds/
• GCA_000269785.2
• GCA_000278405.1
• GCA_000278425.1
• GCA_000320905.1
• GCA_000691885.1
• GCA_000952835.1
• GCA_000956085.1
• GCA_001576635.1
• GCA_001576645.1
• GCA_001576655.1
• GCA_001576715.1
• GCA_001576725.1
• GCA_001576735.1
• GCA_001576745.1
• GCA_001576795.1
• GCA_001695535.1
• GCA_002007945.1
• GCA_002214955.1
• GCA_002214965.1
• GCA_002217615.1
• GCA_002217635.1
• GCA_002443195.2
• GCA_002443215.2
• GCA_002456175.2
• GCA_002864195.1
• GCA_002894705.1
• GCA_003709025.1
• GCA_003711285.1
• GCA_003711305.1
• GCA_003711315.1
• GCA_003711345.1
• GCA_003711355.1
• GCA_003711385.1
• GCA_003953485.1
• GCA_003953495.1
• GCA_003953505.1
• GCA_003953515.1
• GCA_003953525.1
• GCA_003953585.1
• GCA_003953595.1
• GCA_003953605.1
• GCA_003953615.1
• GCA_003953625.1
• GCA_003953685.1
• GCA_003953695.1
• GCA_003953705.1
• GCA_003953715.1
• GCA_003953735.1
• GCA_003953785.1
• GCA_003953795.1
• GCA_003953805.1
• GCA_003953825.1
• GCA_003953865.1
• GCA_003967615.1
• GCA_003967635.1
• GCA_003967655.1
• GCA_003967675.1
• GCA_003967695.1
• GCA_003967715.1
• GCA_003967735.1
• GCA_003967755.1
• GCA_003967775.1
• GCA_003967795.1
• GCA_004329145.1
• GCA_004353305.1
• GCF_000006275.2
• GCF_000184455.2
• run1_AD001_ATCACG
• run1_AD002_CGATGT
• run1_AD003_TTAGGC
• run1_AD004_TGACCA
• run1_AD005_ACAGTG
• run1_AD006_GCCAAT
• run1_AD007_CAGATC
• run1_AD008_ACTTGA
• run1_AD012_CTTGTA
• run1_AD013_AGTCAA
• run1_AD014_AGTTCC
• run2_AD002_CGATGT
• run2_AD004_TGACCA
• run2_AD005_ACAGTG
• run2_AD006_GCCAAT
• run2_AD007_CAGATC
• run2_AD010_TAGCTT
• run2_AD011_GGCTAC
• run2_AD012_CTTGTA
• run2_AD013_AGTCAA
• run2_AD014_AGTTCC
• run2_AD015_ATGTCA
• run2_AD016_CCGTCC
• run2_AD018_GTCCGC
• run2_AD019_GTGAAA
• run2_AD020_GTGGCC
• run2_AD021_GTTTCG
• run2_AD022_CGTACG
• run2_AD023_GAGTGG
• run2_AD025_ACTGAT
• run2_AD027_ATTCCT
• run3_index05_ACAGTG
• run3_index06_GCCAAT
• run3_index07_CAGATC
• run3_index08_ACTTGA
• run3_index09_GATCAG
• run3_index10_TAGCTT
• run3_index11_GGCTAC
• run3_index12_CTTGTA
• run3_index13_AGTCAA
• run3_index14_AGTTCC
• run3_index15_ATGTCA
• run3_index16_CCGTCC
• run3_index18_GTCCGC
• run3_index19_GTGAAA
• run3_index20_GTGGCC
• run3_index21_GTTTCG
• run3_index22_CGTACG
• run3_index23_GAGTGG
• run3_index25_ACTGAT
• run3_index27_ATTCCT
• run4_index01_ATCACG
• run4_index02_CGATGT
• run4_index03_TTAGGC
• run4_index04_TGACCA
• run4_index05_ACAGTG
• run4_index06_GCCAAT
• run4_index08_ACTTGA
• run4_index09_GATCAG
• run4_index10_TAGCTT
• run4_index12_CTTGTA
• run4_index13_AGTCAA
• run4_index14_AGTTCC
• run4_index15_ATGTCA
• run4_index18_GTCCGC
• run4_index19_GTGAAA
• run5_index01_ATCACGAT
• run5_index02_CGATGTAT
• run5_index03_TTAGGCAT
• run5_index04_TGACCAAT
• run5_index05_ACAGTGAT
• run5_index06_GCCAATAT
• run5_index07_CAGATCAT
• run5_index08_ACTTGAAT
• run5_index09_GATCAGAT
• run5_index10_TAGCTTAT
• run5_index11_GGCTACAT
• run5_index12_CTTGTAAT
• run5_index13_AGTCAACA
• run5_index14_AGTTCCGT
• run5_index15_ATGTCAGA
• run5_index16_CCGTCCCG
• run5_index20_GTGGCCTT
• run5_index21_GTTTCGGA
• run5_index27_ATTCCTTT