DATA/
DATA//combo_pipeline.rdata
DATA//RDS
DATA//RDS/pw_bite_1.rds
DATA//RDS/pw_intro_0.rds
DATA//RDS/pw_synth_5.rds
DATA//RDS/pw_da_asv_4.rds
DATA//RDS/pw_prep_2.rds
DATA//RDS/pw_div_3.rds
DATA//SUPPLEMENTARY_FILE
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DATA//SUPPLEMENTARY_FILE/table_S6_links.txt
DATA//SUPPLEMENTARY_FILE/Figure_S1.pdf
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DATA//SUPPLEMENTARY_FILE/table_S7_links.txt
DATA//SUPPLEMENTARY_FILE/OLD
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DATA//SUPPLEMENTARY_FILE/OLD/Table_S6.txt
DATA//SUPPLEMENTARY_FILE/OLD/Table_S4.txt
DATA//SUPPLEMENTARY_FILE/OLD/Table_S5.txt
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DATA//SUPPLEMENTARY_FILE/OLD/Table_S3.txt
DATA//SUPPLEMENTARY_FILE/Table_S2_links.txt
DATA//SUPPLEMENTARY_FILE/table_S7.txt
DATA//SUPPLEMENTARY_FILE/table_S6.txt
DATA//SUPPLEMENTARY_FILE/table_S4.txt
DATA//SUPPLEMENTARY_FILE/table_S5.txt
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DATA//02_MERGED
DATA//02_MERGED/RUN03
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DATA//02_MERGED/pre_combo_pipeline.rdata
DATA//PHYLOSEQ
DATA//PHYLOSEQ/combo_pipeline.rdata
DATA//PHYLOSEQ/FIGURES
DATA//PHYLOSEQ/FIGURES/OUTPUT
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_S1.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/box_and_whisker.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_4B.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_4A.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_1.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_2A.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_2C.pdf
DATA//PHYLOSEQ/FIGURES/OUTPUT/Figure_2B.pdf
DATA//PHYLOSEQ/FIGURES/INPUT
DATA//PHYLOSEQ/FIGURES/INPUT/Figure_3_TreeA_2.svg
DATA//PHYLOSEQ/FIGURES/INPUT/Figure_3_Legend_A 2.svg
DATA//PHYLOSEQ/FIGURES/INPUT/collapse_tree.svg
DATA//PHYLOSEQ/FIGURES/INPUT/Figure_3_Legend_A.svg
DATA//PHYLOSEQ/PS_OBJECTS
DATA//PHYLOSEQ/PS_OBJECTS/ps_slv_work_filt.rds
DATA//PHYLOSEQ/PS_OBJECTS/mergedGP.rds
DATA//PHYLOSEQ/PS_OBJECTS/ps.RData
DATA//PHYLOSEQ/TABLES
DATA//PHYLOSEQ/TABLES/OUTPUT
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP/Table_S6.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP/Table_S4.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP/Table_S5.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP/Table_S1.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/SUPP/Table_S3.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/full_tax_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/trim_tax_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/chloroplast_tax_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/chloroplast_sample_data.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/trim_sample_data.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/full_sample_data.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/chloroplast_seq_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/trim_seq_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/PS/full_seq_table.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/ASV_FOR_BLAST.fasta
DATA//PHYLOSEQ/TABLES/OUTPUT/prop_ASV_reads_by_host.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/OTHER
DATA//PHYLOSEQ/TABLES/OUTPUT/OTHER/ps_slv_work_filt_combine.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/OTHER/seq_tab_for_core.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/OTHER/ps_slv_work_filt.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/BLAST_RESULTS.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/LEfSe
DATA//PHYLOSEQ/TABLES/OUTPUT/LEfSe/LEfSe_INPUT_seq_tab.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/LEfSe/LEfSe_INPUT_tax_tab.txt
DATA//PHYLOSEQ/TABLES/OUTPUT/LEfSe/LEfSe_INPUT_metadata.txt
DATA//PHYLOSEQ/TABLES/INPUT
DATA//PHYLOSEQ/TABLES/INPUT/Mean_bite_characteristics.txt
DATA//PHYLOSEQ/TABLES/INPUT/Table_1.txt
DATA//PHYLOSEQ/TABLES/INPUT/lefse_results.txt
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/item_orders.txt
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/2_da_asv_merged_environmental.txt
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/Gut_microbiome_dendrograms_aug_2019.pdf
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/Phylo_Eco_Mantel_tests.txt
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/Mean_bite_characteristics.csv
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/2_da_asv_merged_fish.txt
DATA//PHYLOSEQ/TABLES/INPUT/MANTEL_TEST/2_da_asv_merged_animal.txt
DATA//PHYLOSEQ/TABLES/INPUT/Table_S7.txt
DATA//PHYLOSEQ/TABLES/INPUT/BLAST_results.txt
DATA//PHYLOSEQ/TABLES/INPUT/host_metrics.txt
DATA//PHYLOSEQ/TABLES/INPUT/habitat_specificity.txt