Loading unaligned sequence data#
We can load unaligned sequence data using the load_unaligned app, this will return a SequenceCollection.
Loading unaligned DNA sequences from a single fasta file#
In this example, we load unaligned DNA sequences from a single fasta file using the load_unaligned app. We specify the molecular type (moltype="protein") and the file format (format="fasta").
from cogent3 import get_app
load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein")
seqs = load_unaligned_app("data/inseqs_protein.fasta")
seqs
| 0 | |
| 1091044_fragment | IPLDFDKEFRDKTVVIVAIPGAFTPT |
| 13541053_fragment | KKKNTEVISVSEDTVYVHKAWVQYD |
| 15605725_fragment | FEILAINMDPENLTGFLKNNP |
3 x {min=21, median=25, max=26} protein sequence collection
Loading unaligned DNA sequences from multiple fasta files#
To load unaligned DNA sequences from multiple fasta files, we need two things, a data store that identifies the files we are interested in and a process composed of our apps of interest.
1. A data store that identifies the files we are interested in#
Here we open a read-only (mode="r") data store that identifies all fasta files in the data directory, limiting the data store to two members as a minimum example.
from cogent3 import get_app, open_data_store
fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2)
2. A composed process that defines our workflow#
In this example, our process loads the unaligned sequences using load_unaligned, then applies jaccard_dist to estimate a kmer-based genetic distance, which we write out to a data store using write_tabular.
Note
Apps that are “writers” require a data store to write to, learn more about writers here!.
out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w")
load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna")
jdist = get_app("jaccard_dist")
writer = get_app("write_tabular", out_dstore, format="tsv")
process = load_unaligned_app + jdist + writer
Tip
When running this code on your machine, remember to replace path_to_dir with an actual directory path.
Now we’re good to go! We can apply process to our data store of fasta sequences. result is a data store, which you can index to see individual data members. We can inspect a given data member using the .read() on data members.
result = process.apply_to(fasta_seq_dstore)
print(result[1].read())
dim-1 dim-2 value
seq_104_Tropheryma_whipplei seq_105_Xylella_fastidiosa 0.9770992366412213
seq_104_Tropheryma_whipplei seq_117_Pseudomonas_syringae_pv._Tomato 1.0
seq_104_Tropheryma_whipplei seq_119_Bacillus_anthracis 0.9770992366412213
seq_104_Tropheryma_whipplei seq_129_Bacillus_anthracis 0.9770992366412213
seq_104_Tropheryma_whipplei seq_130_Geobacter_sulfurreducens 0.9848484848484849
seq_104_Tropheryma_whipplei seq_135_Yersinia_pestis_biovar_Medievalis 1.0
seq_104_Tropheryma_whipplei seq_138_Bacillus_cereus 0.9770992366412213
seq_104_Tropheryma_whipplei seq_146_Bacillus_thuringiensis_serovar_konkukian 0.9770992366412213
seq_104_Tropheryma_whipplei seq_148_Bartonella_quintana 0.9105691056910569
seq_104_Tropheryma_whipplei seq_23_Haemophilus_influenzae 1.0
seq_104_Tropheryma_whipplei seq_24_Campylobacter_jejuni 0.9848484848484849
seq_104_Tropheryma_whipplei seq_31_Pseudomonas_aeruginosa 0.9193548387096774
seq_104_Tropheryma_whipplei seq_46_Salmonella_enterica 1.0
seq_104_Tropheryma_whipplei seq_48_Aeropyrum_pernix 1.0
seq_104_Tropheryma_whipplei seq_50_Halobacterium_sp. 1.0
seq_104_Tropheryma_whipplei seq_59_Thermoplasma_acidophilum 0.9689922480620154
seq_104_Tropheryma_whipplei seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9770992366412213
seq_104_Tropheryma_whipplei seq_86_Xanthomonas_axonopodis_pv._citri. 0.9193548387096774
seq_104_Tropheryma_whipplei seq_95_Shewanella_oneidensis 1.0
seq_105_Xylella_fastidiosa seq_104_Tropheryma_whipplei 0.9770992366412213
seq_105_Xylella_fastidiosa seq_117_Pseudomonas_syringae_pv._Tomato 0.7592592592592593
seq_105_Xylella_fastidiosa seq_119_Bacillus_anthracis 0.8347826086956522
seq_105_Xylella_fastidiosa seq_129_Bacillus_anthracis 0.8347826086956522
seq_105_Xylella_fastidiosa seq_130_Geobacter_sulfurreducens 0.9448818897637795
seq_105_Xylella_fastidiosa seq_135_Yersinia_pestis_biovar_Medievalis 0.7818181818181819
seq_105_Xylella_fastidiosa seq_138_Bacillus_cereus 0.8347826086956522
seq_105_Xylella_fastidiosa seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8347826086956522
seq_105_Xylella_fastidiosa seq_148_Bartonella_quintana 0.9612403100775194
seq_105_Xylella_fastidiosa seq_23_Haemophilus_influenzae 0.7592592592592593
seq_105_Xylella_fastidiosa seq_24_Campylobacter_jejuni 0.8925619834710744
seq_105_Xylella_fastidiosa seq_31_Pseudomonas_aeruginosa 0.8448275862068966
seq_105_Xylella_fastidiosa seq_46_Salmonella_enterica 0.7818181818181819
seq_105_Xylella_fastidiosa seq_48_Aeropyrum_pernix 1.0
seq_105_Xylella_fastidiosa seq_50_Halobacterium_sp. 1.0
seq_105_Xylella_fastidiosa seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_105_Xylella_fastidiosa seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_105_Xylella_fastidiosa seq_86_Xanthomonas_axonopodis_pv._citri. 0.8547008547008547
seq_105_Xylella_fastidiosa seq_95_Shewanella_oneidensis 0.8925619834710744
seq_117_Pseudomonas_syringae_pv._Tomato seq_104_Tropheryma_whipplei 1.0
seq_117_Pseudomonas_syringae_pv._Tomato seq_105_Xylella_fastidiosa 0.7592592592592593
seq_117_Pseudomonas_syringae_pv._Tomato seq_119_Bacillus_anthracis 0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato seq_129_Bacillus_anthracis 0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato seq_130_Geobacter_sulfurreducens 0.6862745098039216
seq_117_Pseudomonas_syringae_pv._Tomato seq_135_Yersinia_pestis_biovar_Medievalis 0.6185567010309279
seq_117_Pseudomonas_syringae_pv._Tomato seq_138_Bacillus_cereus 0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato seq_146_Bacillus_thuringiensis_serovar_konkukian 0.7706422018348624
seq_117_Pseudomonas_syringae_pv._Tomato seq_148_Bartonella_quintana 0.9193548387096774
seq_117_Pseudomonas_syringae_pv._Tomato seq_23_Haemophilus_influenzae 0.5894736842105264
seq_117_Pseudomonas_syringae_pv._Tomato seq_24_Campylobacter_jejuni 0.8925619834710744
seq_117_Pseudomonas_syringae_pv._Tomato seq_31_Pseudomonas_aeruginosa 0.574468085106383
seq_117_Pseudomonas_syringae_pv._Tomato seq_46_Salmonella_enterica 0.6185567010309279
seq_117_Pseudomonas_syringae_pv._Tomato seq_48_Aeropyrum_pernix 1.0
seq_117_Pseudomonas_syringae_pv._Tomato seq_50_Halobacterium_sp. 1.0
seq_117_Pseudomonas_syringae_pv._Tomato seq_59_Thermoplasma_acidophilum 1.0
seq_117_Pseudomonas_syringae_pv._Tomato seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_117_Pseudomonas_syringae_pv._Tomato seq_86_Xanthomonas_axonopodis_pv._citri. 0.5894736842105264
seq_117_Pseudomonas_syringae_pv._Tomato seq_95_Shewanella_oneidensis 0.8347826086956522
seq_119_Bacillus_anthracis seq_104_Tropheryma_whipplei 0.9770992366412213
seq_119_Bacillus_anthracis seq_105_Xylella_fastidiosa 0.8347826086956522
seq_119_Bacillus_anthracis seq_117_Pseudomonas_syringae_pv._Tomato 0.7706422018348624
seq_119_Bacillus_anthracis seq_129_Bacillus_anthracis 0.05797101449275366
seq_119_Bacillus_anthracis seq_130_Geobacter_sulfurreducens 0.5894736842105264
seq_119_Bacillus_anthracis seq_135_Yersinia_pestis_biovar_Medievalis 0.8833333333333333
seq_119_Bacillus_anthracis seq_138_Bacillus_cereus 0.0
seq_119_Bacillus_anthracis seq_146_Bacillus_thuringiensis_serovar_konkukian 0.0
seq_119_Bacillus_anthracis seq_148_Bartonella_quintana 0.9612403100775194
seq_119_Bacillus_anthracis seq_23_Haemophilus_influenzae 0.8833333333333333
seq_119_Bacillus_anthracis seq_24_Campylobacter_jejuni 0.8925619834710744
seq_119_Bacillus_anthracis seq_31_Pseudomonas_aeruginosa 0.8347826086956522
seq_119_Bacillus_anthracis seq_46_Salmonella_enterica 0.8833333333333333
seq_119_Bacillus_anthracis seq_48_Aeropyrum_pernix 1.0
seq_119_Bacillus_anthracis seq_50_Halobacterium_sp. 1.0
seq_119_Bacillus_anthracis seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_119_Bacillus_anthracis seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_119_Bacillus_anthracis seq_86_Xanthomonas_axonopodis_pv._citri. 0.8547008547008547
seq_119_Bacillus_anthracis seq_95_Shewanella_oneidensis 0.7706422018348624
seq_129_Bacillus_anthracis seq_104_Tropheryma_whipplei 0.9770992366412213
seq_129_Bacillus_anthracis seq_105_Xylella_fastidiosa 0.8347826086956522
seq_129_Bacillus_anthracis seq_117_Pseudomonas_syringae_pv._Tomato 0.7706422018348624
seq_129_Bacillus_anthracis seq_119_Bacillus_anthracis 0.05797101449275366
seq_129_Bacillus_anthracis seq_130_Geobacter_sulfurreducens 0.5894736842105264
seq_129_Bacillus_anthracis seq_135_Yersinia_pestis_biovar_Medievalis 0.8833333333333333
seq_129_Bacillus_anthracis seq_138_Bacillus_cereus 0.05797101449275366
seq_129_Bacillus_anthracis seq_146_Bacillus_thuringiensis_serovar_konkukian 0.05797101449275366
seq_129_Bacillus_anthracis seq_148_Bartonella_quintana 0.9612403100775194
seq_129_Bacillus_anthracis seq_23_Haemophilus_influenzae 0.8833333333333333
seq_129_Bacillus_anthracis seq_24_Campylobacter_jejuni 0.8925619834710744
seq_129_Bacillus_anthracis seq_31_Pseudomonas_aeruginosa 0.8347826086956522
seq_129_Bacillus_anthracis seq_46_Salmonella_enterica 0.8833333333333333
seq_129_Bacillus_anthracis seq_48_Aeropyrum_pernix 1.0
seq_129_Bacillus_anthracis seq_50_Halobacterium_sp. 1.0
seq_129_Bacillus_anthracis seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_129_Bacillus_anthracis seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_129_Bacillus_anthracis seq_86_Xanthomonas_axonopodis_pv._citri. 0.8547008547008547
seq_129_Bacillus_anthracis seq_95_Shewanella_oneidensis 0.7706422018348624
seq_130_Geobacter_sulfurreducens seq_104_Tropheryma_whipplei 0.9848484848484849
seq_130_Geobacter_sulfurreducens seq_105_Xylella_fastidiosa 0.9448818897637795
seq_130_Geobacter_sulfurreducens seq_117_Pseudomonas_syringae_pv._Tomato 0.6862745098039216
seq_130_Geobacter_sulfurreducens seq_119_Bacillus_anthracis 0.5894736842105264
seq_130_Geobacter_sulfurreducens seq_129_Bacillus_anthracis 0.5894736842105264
seq_130_Geobacter_sulfurreducens seq_135_Yersinia_pestis_biovar_Medievalis 0.9612403100775194
seq_130_Geobacter_sulfurreducens seq_138_Bacillus_cereus 0.5894736842105264
seq_130_Geobacter_sulfurreducens seq_146_Bacillus_thuringiensis_serovar_konkukian 0.5894736842105264
seq_130_Geobacter_sulfurreducens seq_148_Bartonella_quintana 0.8833333333333333
seq_130_Geobacter_sulfurreducens seq_23_Haemophilus_influenzae 0.9612403100775194
seq_130_Geobacter_sulfurreducens seq_24_Campylobacter_jejuni 0.9692307692307692
seq_130_Geobacter_sulfurreducens seq_31_Pseudomonas_aeruginosa 0.8547008547008547
seq_130_Geobacter_sulfurreducens seq_46_Salmonella_enterica 0.9612403100775194
seq_130_Geobacter_sulfurreducens seq_48_Aeropyrum_pernix 1.0
seq_130_Geobacter_sulfurreducens seq_50_Halobacterium_sp. 1.0
seq_130_Geobacter_sulfurreducens seq_59_Thermoplasma_acidophilum 1.0
seq_130_Geobacter_sulfurreducens seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_130_Geobacter_sulfurreducens seq_86_Xanthomonas_axonopodis_pv._citri. 0.864406779661017
seq_130_Geobacter_sulfurreducens seq_95_Shewanella_oneidensis 0.8739495798319328
seq_135_Yersinia_pestis_biovar_Medievalis seq_104_Tropheryma_whipplei 1.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_105_Xylella_fastidiosa 0.7818181818181819
seq_135_Yersinia_pestis_biovar_Medievalis seq_117_Pseudomonas_syringae_pv._Tomato 0.6185567010309279
seq_135_Yersinia_pestis_biovar_Medievalis seq_119_Bacillus_anthracis 0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis seq_129_Bacillus_anthracis 0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis seq_130_Geobacter_sulfurreducens 0.9612403100775194
seq_135_Yersinia_pestis_biovar_Medievalis seq_138_Bacillus_cereus 0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis seq_148_Bartonella_quintana 0.9770992366412213
seq_135_Yersinia_pestis_biovar_Medievalis seq_23_Haemophilus_influenzae 0.6041666666666667
seq_135_Yersinia_pestis_biovar_Medievalis seq_24_Campylobacter_jejuni 0.8833333333333333
seq_135_Yersinia_pestis_biovar_Medievalis seq_31_Pseudomonas_aeruginosa 0.7706422018348624
seq_135_Yersinia_pestis_biovar_Medievalis seq_46_Salmonella_enterica 0.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_48_Aeropyrum_pernix 1.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_50_Halobacterium_sp. 1.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_59_Thermoplasma_acidophilum 1.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_135_Yersinia_pestis_biovar_Medievalis seq_86_Xanthomonas_axonopodis_pv._citri. 0.7706422018348624
seq_135_Yersinia_pestis_biovar_Medievalis seq_95_Shewanella_oneidensis 0.8245614035087719
seq_138_Bacillus_cereus seq_104_Tropheryma_whipplei 0.9770992366412213
seq_138_Bacillus_cereus seq_105_Xylella_fastidiosa 0.8347826086956522
seq_138_Bacillus_cereus seq_117_Pseudomonas_syringae_pv._Tomato 0.7706422018348624
seq_138_Bacillus_cereus seq_119_Bacillus_anthracis 0.0
seq_138_Bacillus_cereus seq_129_Bacillus_anthracis 0.05797101449275366
seq_138_Bacillus_cereus seq_130_Geobacter_sulfurreducens 0.5894736842105264
seq_138_Bacillus_cereus seq_135_Yersinia_pestis_biovar_Medievalis 0.8833333333333333
seq_138_Bacillus_cereus seq_146_Bacillus_thuringiensis_serovar_konkukian 0.0
seq_138_Bacillus_cereus seq_148_Bartonella_quintana 0.9612403100775194
seq_138_Bacillus_cereus seq_23_Haemophilus_influenzae 0.8833333333333333
seq_138_Bacillus_cereus seq_24_Campylobacter_jejuni 0.8925619834710744
seq_138_Bacillus_cereus seq_31_Pseudomonas_aeruginosa 0.8347826086956522
seq_138_Bacillus_cereus seq_46_Salmonella_enterica 0.8833333333333333
seq_138_Bacillus_cereus seq_48_Aeropyrum_pernix 1.0
seq_138_Bacillus_cereus seq_50_Halobacterium_sp. 1.0
seq_138_Bacillus_cereus seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_138_Bacillus_cereus seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_138_Bacillus_cereus seq_86_Xanthomonas_axonopodis_pv._citri. 0.8547008547008547
seq_138_Bacillus_cereus seq_95_Shewanella_oneidensis 0.7706422018348624
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_104_Tropheryma_whipplei 0.9770992366412213
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_105_Xylella_fastidiosa 0.8347826086956522
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_117_Pseudomonas_syringae_pv._Tomato 0.7706422018348624
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_119_Bacillus_anthracis 0.0
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_129_Bacillus_anthracis 0.05797101449275366
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_130_Geobacter_sulfurreducens 0.5894736842105264
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_135_Yersinia_pestis_biovar_Medievalis 0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_138_Bacillus_cereus 0.0
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_148_Bartonella_quintana 0.9612403100775194
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_23_Haemophilus_influenzae 0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_24_Campylobacter_jejuni 0.8925619834710744
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_31_Pseudomonas_aeruginosa 0.8347826086956522
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_46_Salmonella_enterica 0.8833333333333333
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_48_Aeropyrum_pernix 1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_50_Halobacterium_sp. 1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_86_Xanthomonas_axonopodis_pv._citri. 0.8547008547008547
seq_146_Bacillus_thuringiensis_serovar_konkukian seq_95_Shewanella_oneidensis 0.7706422018348624
seq_148_Bartonella_quintana seq_104_Tropheryma_whipplei 0.9105691056910569
seq_148_Bartonella_quintana seq_105_Xylella_fastidiosa 0.9612403100775194
seq_148_Bartonella_quintana seq_117_Pseudomonas_syringae_pv._Tomato 0.9193548387096774
seq_148_Bartonella_quintana seq_119_Bacillus_anthracis 0.9612403100775194
seq_148_Bartonella_quintana seq_129_Bacillus_anthracis 0.9612403100775194
seq_148_Bartonella_quintana seq_130_Geobacter_sulfurreducens 0.8833333333333333
seq_148_Bartonella_quintana seq_135_Yersinia_pestis_biovar_Medievalis 0.9770992366412213
seq_148_Bartonella_quintana seq_138_Bacillus_cereus 0.9612403100775194
seq_148_Bartonella_quintana seq_146_Bacillus_thuringiensis_serovar_konkukian 0.9612403100775194
seq_148_Bartonella_quintana seq_23_Haemophilus_influenzae 0.9770992366412213
seq_148_Bartonella_quintana seq_24_Campylobacter_jejuni 0.953125
seq_148_Bartonella_quintana seq_31_Pseudomonas_aeruginosa 0.9016393442622951
seq_148_Bartonella_quintana seq_46_Salmonella_enterica 0.9770992366412213
seq_148_Bartonella_quintana seq_48_Aeropyrum_pernix 0.9847328244274809
seq_148_Bartonella_quintana seq_50_Halobacterium_sp. 1.0
seq_148_Bartonella_quintana seq_59_Thermoplasma_acidophilum 0.9769230769230769
seq_148_Bartonella_quintana seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9770992366412213
seq_148_Bartonella_quintana seq_86_Xanthomonas_axonopodis_pv._citri. 0.9105691056910569
seq_148_Bartonella_quintana seq_95_Shewanella_oneidensis 0.9848484848484849
seq_23_Haemophilus_influenzae seq_104_Tropheryma_whipplei 1.0
seq_23_Haemophilus_influenzae seq_105_Xylella_fastidiosa 0.7592592592592593
seq_23_Haemophilus_influenzae seq_117_Pseudomonas_syringae_pv._Tomato 0.5894736842105264
seq_23_Haemophilus_influenzae seq_119_Bacillus_anthracis 0.8833333333333333
seq_23_Haemophilus_influenzae seq_129_Bacillus_anthracis 0.8833333333333333
seq_23_Haemophilus_influenzae seq_130_Geobacter_sulfurreducens 0.9612403100775194
seq_23_Haemophilus_influenzae seq_135_Yersinia_pestis_biovar_Medievalis 0.6041666666666667
seq_23_Haemophilus_influenzae seq_138_Bacillus_cereus 0.8833333333333333
seq_23_Haemophilus_influenzae seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8833333333333333
seq_23_Haemophilus_influenzae seq_148_Bartonella_quintana 0.9770992366412213
seq_23_Haemophilus_influenzae seq_24_Campylobacter_jejuni 0.8925619834710744
seq_23_Haemophilus_influenzae seq_31_Pseudomonas_aeruginosa 0.7476635514018692
seq_23_Haemophilus_influenzae seq_46_Salmonella_enterica 0.6041666666666667
seq_23_Haemophilus_influenzae seq_48_Aeropyrum_pernix 1.0
seq_23_Haemophilus_influenzae seq_50_Halobacterium_sp. 1.0
seq_23_Haemophilus_influenzae seq_59_Thermoplasma_acidophilum 1.0
seq_23_Haemophilus_influenzae seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_23_Haemophilus_influenzae seq_86_Xanthomonas_axonopodis_pv._citri. 0.7476635514018692
seq_23_Haemophilus_influenzae seq_95_Shewanella_oneidensis 0.8245614035087719
seq_24_Campylobacter_jejuni seq_104_Tropheryma_whipplei 0.9848484848484849
seq_24_Campylobacter_jejuni seq_105_Xylella_fastidiosa 0.8925619834710744
seq_24_Campylobacter_jejuni seq_117_Pseudomonas_syringae_pv._Tomato 0.8925619834710744
seq_24_Campylobacter_jejuni seq_119_Bacillus_anthracis 0.8925619834710744
seq_24_Campylobacter_jejuni seq_129_Bacillus_anthracis 0.8925619834710744
seq_24_Campylobacter_jejuni seq_130_Geobacter_sulfurreducens 0.9692307692307692
seq_24_Campylobacter_jejuni seq_135_Yersinia_pestis_biovar_Medievalis 0.8833333333333333
seq_24_Campylobacter_jejuni seq_138_Bacillus_cereus 0.8925619834710744
seq_24_Campylobacter_jejuni seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8925619834710744
seq_24_Campylobacter_jejuni seq_148_Bartonella_quintana 0.953125
seq_24_Campylobacter_jejuni seq_23_Haemophilus_influenzae 0.8925619834710744
seq_24_Campylobacter_jejuni seq_31_Pseudomonas_aeruginosa 0.9924812030075187
seq_24_Campylobacter_jejuni seq_46_Salmonella_enterica 0.8833333333333333
seq_24_Campylobacter_jejuni seq_48_Aeropyrum_pernix 1.0
seq_24_Campylobacter_jejuni seq_50_Halobacterium_sp. 1.0
seq_24_Campylobacter_jejuni seq_59_Thermoplasma_acidophilum 1.0
seq_24_Campylobacter_jejuni seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_24_Campylobacter_jejuni seq_86_Xanthomonas_axonopodis_pv._citri. 0.9924812030075187
seq_24_Campylobacter_jejuni seq_95_Shewanella_oneidensis 0.9016393442622951
seq_31_Pseudomonas_aeruginosa seq_104_Tropheryma_whipplei 0.9193548387096774
seq_31_Pseudomonas_aeruginosa seq_105_Xylella_fastidiosa 0.8448275862068966
seq_31_Pseudomonas_aeruginosa seq_117_Pseudomonas_syringae_pv._Tomato 0.574468085106383
seq_31_Pseudomonas_aeruginosa seq_119_Bacillus_anthracis 0.8347826086956522
seq_31_Pseudomonas_aeruginosa seq_129_Bacillus_anthracis 0.8347826086956522
seq_31_Pseudomonas_aeruginosa seq_130_Geobacter_sulfurreducens 0.8547008547008547
seq_31_Pseudomonas_aeruginosa seq_135_Yersinia_pestis_biovar_Medievalis 0.7706422018348624
seq_31_Pseudomonas_aeruginosa seq_138_Bacillus_cereus 0.8347826086956522
seq_31_Pseudomonas_aeruginosa seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8347826086956522
seq_31_Pseudomonas_aeruginosa seq_148_Bartonella_quintana 0.9016393442622951
seq_31_Pseudomonas_aeruginosa seq_23_Haemophilus_influenzae 0.7476635514018692
seq_31_Pseudomonas_aeruginosa seq_24_Campylobacter_jejuni 0.9924812030075187
seq_31_Pseudomonas_aeruginosa seq_46_Salmonella_enterica 0.7706422018348624
seq_31_Pseudomonas_aeruginosa seq_48_Aeropyrum_pernix 1.0
seq_31_Pseudomonas_aeruginosa seq_50_Halobacterium_sp. 1.0
seq_31_Pseudomonas_aeruginosa seq_59_Thermoplasma_acidophilum 0.9609375
seq_31_Pseudomonas_aeruginosa seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9770992366412213
seq_31_Pseudomonas_aeruginosa seq_86_Xanthomonas_axonopodis_pv._citri. 0.3855421686746988
seq_31_Pseudomonas_aeruginosa seq_95_Shewanella_oneidensis 0.9365079365079365
seq_46_Salmonella_enterica seq_104_Tropheryma_whipplei 1.0
seq_46_Salmonella_enterica seq_105_Xylella_fastidiosa 0.7818181818181819
seq_46_Salmonella_enterica seq_117_Pseudomonas_syringae_pv._Tomato 0.6185567010309279
seq_46_Salmonella_enterica seq_119_Bacillus_anthracis 0.8833333333333333
seq_46_Salmonella_enterica seq_129_Bacillus_anthracis 0.8833333333333333
seq_46_Salmonella_enterica seq_130_Geobacter_sulfurreducens 0.9612403100775194
seq_46_Salmonella_enterica seq_135_Yersinia_pestis_biovar_Medievalis 0.0
seq_46_Salmonella_enterica seq_138_Bacillus_cereus 0.8833333333333333
seq_46_Salmonella_enterica seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8833333333333333
seq_46_Salmonella_enterica seq_148_Bartonella_quintana 0.9770992366412213
seq_46_Salmonella_enterica seq_23_Haemophilus_influenzae 0.6041666666666667
seq_46_Salmonella_enterica seq_24_Campylobacter_jejuni 0.8833333333333333
seq_46_Salmonella_enterica seq_31_Pseudomonas_aeruginosa 0.7706422018348624
seq_46_Salmonella_enterica seq_48_Aeropyrum_pernix 1.0
seq_46_Salmonella_enterica seq_50_Halobacterium_sp. 1.0
seq_46_Salmonella_enterica seq_59_Thermoplasma_acidophilum 1.0
seq_46_Salmonella_enterica seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_46_Salmonella_enterica seq_86_Xanthomonas_axonopodis_pv._citri. 0.7706422018348624
seq_46_Salmonella_enterica seq_95_Shewanella_oneidensis 0.8245614035087719
seq_48_Aeropyrum_pernix seq_104_Tropheryma_whipplei 1.0
seq_48_Aeropyrum_pernix seq_105_Xylella_fastidiosa 1.0
seq_48_Aeropyrum_pernix seq_117_Pseudomonas_syringae_pv._Tomato 1.0
seq_48_Aeropyrum_pernix seq_119_Bacillus_anthracis 1.0
seq_48_Aeropyrum_pernix seq_129_Bacillus_anthracis 1.0
seq_48_Aeropyrum_pernix seq_130_Geobacter_sulfurreducens 1.0
seq_48_Aeropyrum_pernix seq_135_Yersinia_pestis_biovar_Medievalis 1.0
seq_48_Aeropyrum_pernix seq_138_Bacillus_cereus 1.0
seq_48_Aeropyrum_pernix seq_146_Bacillus_thuringiensis_serovar_konkukian 1.0
seq_48_Aeropyrum_pernix seq_148_Bartonella_quintana 0.9847328244274809
seq_48_Aeropyrum_pernix seq_23_Haemophilus_influenzae 1.0
seq_48_Aeropyrum_pernix seq_24_Campylobacter_jejuni 1.0
seq_48_Aeropyrum_pernix seq_31_Pseudomonas_aeruginosa 1.0
seq_48_Aeropyrum_pernix seq_46_Salmonella_enterica 1.0
seq_48_Aeropyrum_pernix seq_50_Halobacterium_sp. 1.0
seq_48_Aeropyrum_pernix seq_59_Thermoplasma_acidophilum 0.9846153846153847
seq_48_Aeropyrum_pernix seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9847328244274809
seq_48_Aeropyrum_pernix seq_86_Xanthomonas_axonopodis_pv._citri. 1.0
seq_48_Aeropyrum_pernix seq_95_Shewanella_oneidensis 1.0
seq_50_Halobacterium_sp. seq_104_Tropheryma_whipplei 1.0
seq_50_Halobacterium_sp. seq_105_Xylella_fastidiosa 1.0
seq_50_Halobacterium_sp. seq_117_Pseudomonas_syringae_pv._Tomato 1.0
seq_50_Halobacterium_sp. seq_119_Bacillus_anthracis 1.0
seq_50_Halobacterium_sp. seq_129_Bacillus_anthracis 1.0
seq_50_Halobacterium_sp. seq_130_Geobacter_sulfurreducens 1.0
seq_50_Halobacterium_sp. seq_135_Yersinia_pestis_biovar_Medievalis 1.0
seq_50_Halobacterium_sp. seq_138_Bacillus_cereus 1.0
seq_50_Halobacterium_sp. seq_146_Bacillus_thuringiensis_serovar_konkukian 1.0
seq_50_Halobacterium_sp. seq_148_Bartonella_quintana 1.0
seq_50_Halobacterium_sp. seq_23_Haemophilus_influenzae 1.0
seq_50_Halobacterium_sp. seq_24_Campylobacter_jejuni 1.0
seq_50_Halobacterium_sp. seq_31_Pseudomonas_aeruginosa 1.0
seq_50_Halobacterium_sp. seq_46_Salmonella_enterica 1.0
seq_50_Halobacterium_sp. seq_48_Aeropyrum_pernix 1.0
seq_50_Halobacterium_sp. seq_59_Thermoplasma_acidophilum 0.9847328244274809
seq_50_Halobacterium_sp. seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9848484848484849
seq_50_Halobacterium_sp. seq_86_Xanthomonas_axonopodis_pv._citri. 1.0
seq_50_Halobacterium_sp. seq_95_Shewanella_oneidensis 0.9770992366412213
seq_59_Thermoplasma_acidophilum seq_104_Tropheryma_whipplei 0.9689922480620154
seq_59_Thermoplasma_acidophilum seq_105_Xylella_fastidiosa 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_117_Pseudomonas_syringae_pv._Tomato 1.0
seq_59_Thermoplasma_acidophilum seq_119_Bacillus_anthracis 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_129_Bacillus_anthracis 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_130_Geobacter_sulfurreducens 1.0
seq_59_Thermoplasma_acidophilum seq_135_Yersinia_pestis_biovar_Medievalis 1.0
seq_59_Thermoplasma_acidophilum seq_138_Bacillus_cereus 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_146_Bacillus_thuringiensis_serovar_konkukian 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_148_Bartonella_quintana 0.9769230769230769
seq_59_Thermoplasma_acidophilum seq_23_Haemophilus_influenzae 1.0
seq_59_Thermoplasma_acidophilum seq_24_Campylobacter_jejuni 1.0
seq_59_Thermoplasma_acidophilum seq_31_Pseudomonas_aeruginosa 0.9609375
seq_59_Thermoplasma_acidophilum seq_46_Salmonella_enterica 1.0
seq_59_Thermoplasma_acidophilum seq_48_Aeropyrum_pernix 0.9846153846153847
seq_59_Thermoplasma_acidophilum seq_50_Halobacterium_sp. 0.9847328244274809
seq_59_Thermoplasma_acidophilum seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.6831683168316831
seq_59_Thermoplasma_acidophilum seq_86_Xanthomonas_axonopodis_pv._citri. 0.9689922480620154
seq_59_Thermoplasma_acidophilum seq_95_Shewanella_oneidensis 0.9924242424242424
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_104_Tropheryma_whipplei 0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_105_Xylella_fastidiosa 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_117_Pseudomonas_syringae_pv._Tomato 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_119_Bacillus_anthracis 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_129_Bacillus_anthracis 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_130_Geobacter_sulfurreducens 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_135_Yersinia_pestis_biovar_Medievalis 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_138_Bacillus_cereus 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_146_Bacillus_thuringiensis_serovar_konkukian 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_148_Bartonella_quintana 0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_23_Haemophilus_influenzae 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_24_Campylobacter_jejuni 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_31_Pseudomonas_aeruginosa 0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_46_Salmonella_enterica 1.0
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_48_Aeropyrum_pernix 0.9847328244274809
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_50_Halobacterium_sp. 0.9848484848484849
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_59_Thermoplasma_acidophilum 0.6831683168316831
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_86_Xanthomonas_axonopodis_pv._citri. 0.9770992366412213
seq_70_Saccharomyces_cerevisiae_(baker's_yeast) seq_95_Shewanella_oneidensis 1.0
seq_86_Xanthomonas_axonopodis_pv._citri. seq_104_Tropheryma_whipplei 0.9193548387096774
seq_86_Xanthomonas_axonopodis_pv._citri. seq_105_Xylella_fastidiosa 0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri. seq_117_Pseudomonas_syringae_pv._Tomato 0.5894736842105264
seq_86_Xanthomonas_axonopodis_pv._citri. seq_119_Bacillus_anthracis 0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri. seq_129_Bacillus_anthracis 0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri. seq_130_Geobacter_sulfurreducens 0.864406779661017
seq_86_Xanthomonas_axonopodis_pv._citri. seq_135_Yersinia_pestis_biovar_Medievalis 0.7706422018348624
seq_86_Xanthomonas_axonopodis_pv._citri. seq_138_Bacillus_cereus 0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri. seq_146_Bacillus_thuringiensis_serovar_konkukian 0.8547008547008547
seq_86_Xanthomonas_axonopodis_pv._citri. seq_148_Bartonella_quintana 0.9105691056910569
seq_86_Xanthomonas_axonopodis_pv._citri. seq_23_Haemophilus_influenzae 0.7476635514018692
seq_86_Xanthomonas_axonopodis_pv._citri. seq_24_Campylobacter_jejuni 0.9924812030075187
seq_86_Xanthomonas_axonopodis_pv._citri. seq_31_Pseudomonas_aeruginosa 0.3855421686746988
seq_86_Xanthomonas_axonopodis_pv._citri. seq_46_Salmonella_enterica 0.7706422018348624
seq_86_Xanthomonas_axonopodis_pv._citri. seq_48_Aeropyrum_pernix 1.0
seq_86_Xanthomonas_axonopodis_pv._citri. seq_50_Halobacterium_sp. 1.0
seq_86_Xanthomonas_axonopodis_pv._citri. seq_59_Thermoplasma_acidophilum 0.9689922480620154
seq_86_Xanthomonas_axonopodis_pv._citri. seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 0.9770992366412213
seq_86_Xanthomonas_axonopodis_pv._citri. seq_95_Shewanella_oneidensis 0.9365079365079365
seq_95_Shewanella_oneidensis seq_104_Tropheryma_whipplei 1.0
seq_95_Shewanella_oneidensis seq_105_Xylella_fastidiosa 0.8925619834710744
seq_95_Shewanella_oneidensis seq_117_Pseudomonas_syringae_pv._Tomato 0.8347826086956522
seq_95_Shewanella_oneidensis seq_119_Bacillus_anthracis 0.7706422018348624
seq_95_Shewanella_oneidensis seq_129_Bacillus_anthracis 0.7706422018348624
seq_95_Shewanella_oneidensis seq_130_Geobacter_sulfurreducens 0.8739495798319328
seq_95_Shewanella_oneidensis seq_135_Yersinia_pestis_biovar_Medievalis 0.8245614035087719
seq_95_Shewanella_oneidensis seq_138_Bacillus_cereus 0.7706422018348624
seq_95_Shewanella_oneidensis seq_146_Bacillus_thuringiensis_serovar_konkukian 0.7706422018348624
seq_95_Shewanella_oneidensis seq_148_Bartonella_quintana 0.9848484848484849
seq_95_Shewanella_oneidensis seq_23_Haemophilus_influenzae 0.8245614035087719
seq_95_Shewanella_oneidensis seq_24_Campylobacter_jejuni 0.9016393442622951
seq_95_Shewanella_oneidensis seq_31_Pseudomonas_aeruginosa 0.9365079365079365
seq_95_Shewanella_oneidensis seq_46_Salmonella_enterica 0.8245614035087719
seq_95_Shewanella_oneidensis seq_48_Aeropyrum_pernix 1.0
seq_95_Shewanella_oneidensis seq_50_Halobacterium_sp. 0.9770992366412213
seq_95_Shewanella_oneidensis seq_59_Thermoplasma_acidophilum 0.9924242424242424
seq_95_Shewanella_oneidensis seq_70_Saccharomyces_cerevisiae_(baker's_yeast) 1.0
seq_95_Shewanella_oneidensis seq_86_Xanthomonas_axonopodis_pv._citri. 0.9365079365079365