WZA2andWZA1-blast-protein-aln-and-tree (for Fig S7)
RNAseq
core_alignment
in-silico-docking
filename.txt
panaroo
phenotypes
scoary_with_plasmid_amr
selection-alignments
wza2_alignment
wza2_wzaCA_gfcE_alignment (for Fig S6)

./WZA2andWZA1-blast-protein-aln-and-tree (for Fig S7):
FIGS9-WZA2andWZA1-protein.aln.fasta
FIGS9-WZA2andWZA1-protein.aln.nwk

./RNAseq:
5032-GCA014935805_DEgenes.xlsx
5032-GCA019212205_DEgenes.xlsx
5032-GCA020413045_DEgenes.xlsx
5032D-GCA_014935805.1-Report.html
5032D-GCA_014935805.1.star.multiqc.report.html
5032D-GCA_014935805.1_rawCounts.txt
5032D-GCA_019212205.1-Report.html
5032D-GCA_019212205.1.star.multiqc.report.html
5032D-GCA_019212205.1_rawCounts.txt
5032D-GCA_020413045.1-Report.html
5032D-GCA_020413045.1.star.multiqc.report.html
5032D-GCA_020413045.1_rawCounts.txt

./in-silico-docking
2j58-wza with cefo dock (full cube) 3892932 Pose 1.pdf
2j58-wza with cefo dock (full cube) 3892932 Pose 2.pdf
5659 wza-2 no SP with cefo dock (full cube) Pose 1.pdf
5659 wza-2 no SP with cefo dock (full cube) Pose 2.pdf
7593-gfcE no SP with cefo dock (full cube) Pose 1.pdf
7593-gfcE no SP with cefo dock (full cube) Pose 2.pdf
Docking figure.tif

./core_alignment:
genome.tree
hierbaps_clean.txt
sample_metadata.txt

./panaroo:
gene_data.csv
gene_data.zip
gene_position
gene_presence_absence.csv
gene_presence_absence_roary.csv
pan_genome_reference.fa

./phenotypes:
pheno601Dogs_cleaned.csv

./scoary_with_plasmid_amr:
Amikacin.INT_08_02_2022_1720.results.csv
Amoxicillin.Clavulanic.Acid.INT_08_02_2022_1720.results.csv
Amoxicillin.INT_08_02_2022_1720.results.csv
Ampicillin.INT_08_02_2022_1720.results.csv
Cefazolin.INT_08_02_2022_1720.results.csv
Cefovecin.INT_08_02_2022_1720.results.csv
Cefoxitin.INT_08_02_2022_1720.results.csv
Cefpodoxime.INT_08_02_2022_1720.results.csv
Ceftazidime.INT_08_02_2022_1720.results.csv
Ceftiofur.INT_08_02_2022_1720.results.csv
Cephalexin_Comb.INT_08_02_2022_1720.results.csv
Cephalothin.INT_08_02_2022_1720.results.csv
Chloramphenicol.INT_08_02_2022_1720.results.csv
Clindamycin.INT_08_02_2022_1720.results.csv
Doxycycline.INT_08_02_2022_1720.results.csv
Enrofloxacin.INT_08_02_2022_1720.results.csv
Erythromycin.INT_08_02_2022_1720.results.csv
Imipenem.INT_08_02_2022_1720.results.csv
Marbofloxacin.INT_08_02_2022_1720.results.csv
Neomycin.INT_08_02_2022_1720.results.csv
Nitrofurantoin.INT_08_02_2022_1720.results.csv
Orbifloxacin.INT_08_02_2022_1720.results.csv
Oxacillin...2..NaCl.INT_08_02_2022_1720.results.csv
Penicillin.G.INT_08_02_2022_1720.results.csv
Penicillin.INT_08_02_2022_1720.results.csv
Piperacillin.INT_08_02_2022_1720.results.csv
Piperacillin.Tazobactam.INT_08_02_2022_1720.results.csv
Polymyxin.B.INT_08_02_2022_1720.results.csv
Pradofloxacin.INT_08_02_2022_1720.results.csv
Tetracycline.INT_08_02_2022_1720.results.csv
Ticarcillin.Clavulanic.Acid.INT_08_02_2022_1720.results.csv
Ticarcillin.INT_08_02_2022_1720.results.csv
Tobramycin.INT_08_02_2022_1720.results.csv
Trimethoprim.Sulfamethoxazole.INT_08_02_2022_1720.results.csv
merged

./selection-alignments:
wza2-wza1
wza2-wzaCA
wzaCA-gfcE
wzaCA-wza1
wzi-other-wzi

./selection-alignments/wza2-wza1:
wza2-wza1.fasta_protein.aligned.compressed.codon.fas
wza2-wza1.fasta_protein.aligned.compressed.codon.fas.best-gard
wza2-wza1.fasta_protein.aligned.compressed.codon_1.fas
wza2-wza1.fasta_protein.aligned.compressed.codon_1.fas.RELAX.wza2-wza1.json
wza2-wza1.fasta_protein.aligned.compressed.codon_1.fas.raxml.label.bestTree
wza2-wza1.fasta_protein.aligned.compressed.codon_2.fas
wza2-wza1.fasta_protein.aligned.compressed.codon_2.fas.RELAX.wza2-wza1.json
wza2-wza1.fasta_protein.aligned.compressed.codon_2.fas.raxml.label.bestTree
wza2-wza1.fasta_protein.aligned.compressed.codon_3.fas
wza2-wza1.fasta_protein.aligned.compressed.codon_3.fas.RELAX.wza2-wza1.json
wza2-wza1.fasta_protein.aligned.compressed.codon_3.fas.raxml.label.bestTree
wza2-wza1.fasta_protein.aligned.compressed.codon_4.fas
wza2-wza1.fasta_protein.aligned.compressed.codon_4.fas.RELAX.wza2-wza1.json
wza2-wza1.fasta_protein.aligned.compressed.codon_4.fas.raxml.label.bestTree
wza2-wza1.fasta_protein.aligned.compressed.codon_5.fas
wza2-wza1.fasta_protein.aligned.compressed.codon_5.fas.RELAX.wza2-wza1.json
wza2-wza1.fasta_protein.aligned.compressed.codon_5.fas.raxml.label.bestTree

./selection-alignments/wza2-wzaCA:
WZA-WZA2.fasta_protein.aligned.compressed.codon.fas
wzaCA-wza2.fasta.1.fasta_protein.aligned.compressed.codon.C.fas
wzaCA-wza2.fasta.1.fasta_protein.aligned.compressed.codon.C.fas.RELAX.wzaCA-wza2.json
wzaCA-wza2.fasta.1.fasta_protein.aligned.compressed.codon.C.fas.label.raxml.bestTree
wzaCA-wza2.fasta.2.fasta_protein.aligned.compressed.codon.C.fas
wzaCA-wza2.fasta.2.fasta_protein.aligned.compressed.codon.C.fas.RELAX.wzaCA-wza2.json
wzaCA-wza2.fasta.2.fasta_protein.aligned.compressed.codon.C.fas.label.raxml.bestTree
wzaCA-wza2.fasta_protein.aligned.compressed.codon.fas_protein.aligned.compressed.codon.fas.best-gard

./selection-alignments/wzaCA-gfcE:
wzaCA-gfcE.fasta_protein.aligned.compressed.codon.fas
wzaCA-gfcE.fasta_protein.aligned.compressed.codon.fas.best-gard
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_1.fas
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_1.fas.RELAX.wzaCA-gfcE.json
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_1.fas.raxml.label.bestTree
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_2.fas
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_2.fas.RELAX.wzaCA-gfcE.json
wzaCA-gfcE.fasta_protein.aligned.compressed.codon_2.fas.raxml.label.bestTree

./selection-alignments/wzaCA-wza1:
wzaCA-wza1.fasta_protein.aligned.compressed.codon.fas
wzaCA-wza1.fasta_protein.aligned.compressed.codon.fas.best-gard
wzaCA-wza1.fasta_protein.aligned.compressed.codon_1.fas
wzaCA-wza1.fasta_protein.aligned.compressed.codon_1.fas.RELAX.wzaCA-wza1.json
wzaCA-wza1.fasta_protein.aligned.compressed.codon_1.fas.raxml.label.bestTree
wzaCA-wza1.fasta_protein.aligned.compressed.codon_2.fas
wzaCA-wza1.fasta_protein.aligned.compressed.codon_2.fas.RELAX.wzaCA-wza1.json
wzaCA-wza1.fasta_protein.aligned.compressed.codon_2.fas.raxml.label.bestTree

./selection-alignments/wzi-other-wzi:
WZI-Jan8.codon.fas_protein.aligned.compressed.codon.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon.fas.best-gard
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_1.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_1.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_1.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_1.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_2.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_2.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_2.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_2.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_3.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_3.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_3.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_3.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_4.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_4.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_4.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_4.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_5.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_5.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_5.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_5.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_6.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_6.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_6.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_6.fas.raxml.labeled.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_7.fas
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_7.fas.RELAX.wzi-v-wziOUT.Jan9.json
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_7.fas.raxml.bestTree
WZI-Jan8.codon.fas_protein.aligned.compressed.codon_7.fas.raxml.labeled.bestTree

./wza2_alignment:
group_5659.fasta
group_5659_genomes.txt

./wza2_wzaCA_gfcE_alignment (for Fig S6):
dog-5659-7593-7595-align
dog-5659-7593-7595-tre