MANIFEST.in
README.md
README.rst
setup.py
traitar/PhenotypeCollection.py
traitar/__init__.py
traitar/_version.py
traitar/domtblout2gene_generic.py
traitar/evaluation.py
traitar/get_external_data.py
traitar/heatmap.py
traitar/hmm2gff.py
traitar/hmmer2filtered_best.py
traitar/merge_preds.py
traitar/modify.py
traitar/predict.py
traitar/traitar
traitar.egg-info/PKG-INFO
traitar.egg-info/SOURCES.txt
traitar.egg-info/dependency_links.txt
traitar.egg-info/not-zip-safe
traitar.egg-info/requires.txt
traitar.egg-info/top_level.txt
traitar/data/colors.txt
traitar/data/models/phypat+PGL.tar.gz
traitar/data/models/phypat.tar.gz
traitar/data/models/pt2acc.txt
traitar/data/sample_data/1457190.3.RefSeq.faa
traitar/data/sample_data/1457190.3.RefSeq.gff
traitar/data/sample_data/525367.9.RefSeq.faa
traitar/data/sample_data/525367.9.RefSeq.gff
traitar/data/sample_data/samples.txt
traitar/data/sample_data/samples_gene_gff.txt
traitar/data/sample_data/traitar_out/annotation/pfam/Listeria_grayi_DSM_20601_domtblout.dat
traitar/data/sample_data/traitar_out/annotation/pfam/Listeria_grayi_DSM_20601_filtered_best.dat
traitar/data/sample_data/traitar_out/annotation/pfam/Listeria_ivanovii_WSLC3009_domtblout.dat
traitar/data/sample_data/traitar_out/annotation/pfam/Listeria_ivanovii_WSLC3009_filtered_best.dat
traitar/data/sample_data/traitar_out/annotation/pfam/joblog_filter_and_aggregate.txt
traitar/data/sample_data/traitar_out/annotation/pfam/joblog_filter_and_aggregate_recompute.txt
traitar/data/sample_data/traitar_out/annotation/pfam/joblog_generate_annotation_matrix.txt
traitar/data/sample_data/traitar_out/annotation/pfam/joblog_hmmer.txt
traitar/data/sample_data/traitar_out/annotation/pfam/joblog_hmmer_recompute.txt
traitar/data/sample_data/traitar_out/annotation/pfam/summary.dat
traitar/data/sample_data/traitar_out/phenotype_prediction/feature_track_commands.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_combined.png
traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_phypat+PGL.png
traitar/data/sample_data/traitar_out/phenotype_prediction/heatmap_phypat.png
traitar/data/sample_data/traitar_out/phenotype_prediction/predictions_flat_majority-votes_combined.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/predictions_flat_single-votes_combined.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/predictions_majority-vote_combined.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/predictions_single-votes_combined.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/predictions_conservative-vote.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/predictions_majority-vote.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/predictions_raw.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/predictions_single-votes.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/predictions_conservative-vote.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/predictions_majority-vote.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/predictions_raw.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/predictions_single-votes.txt
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Acetate_utilization_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Alkaline_phosphatase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Catalase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Citrate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Coagulase_production_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_D-Mannitol_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_D-Mannose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_DNase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Esculin_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Facultative_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Glucose_fermenter_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Gram_positive_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Growth_at_42°C_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Growth_in_6.5%_NaCl_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Growth_in_KCN_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Growth_on_ordinary_blood_agar_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Lactose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Malonate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Maltose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Motile_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Salicin_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Starch_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Trehalose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_Voges_Proskauer_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_complete_annotation.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_grayi_DSM_20601_important_features.dat
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Acetate_utilization_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Alkaline_phosphatase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Arginine_dihydrolase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Bacillus_or_coccobacillus_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Catalase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Coagulase_production_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_D-Sorbitol_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Esculin_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Facultative_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Glucose_fermenter_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Gram_positive_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_at_42°C_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_in_6.5%_NaCl_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_in_KCN_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_on_ordinary_blood_agar_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Lactose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Malonate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Maltose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Methyl_red_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Motile_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Salicin_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Starch_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Trehalose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_Voges_Proskauer_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_complete_annotation.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat+PGL/feat_gffs/Listeria_ivanovii_WSLC3009_important_features.dat
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Acetate_utilization_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Alkaline_phosphatase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Catalase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Citrate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Coagulase_production_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_D-Mannitol_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_D-Mannose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_DNase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Esculin_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Facultative_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Glucose_fermenter_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Gram_positive_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Growth_at_42°C_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Growth_in_6.5%_NaCl_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Growth_in_KCN_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Growth_on_ordinary_blood_agar_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Lactose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Malonate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Maltose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Motile_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Salicin_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Starch_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Trehalose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_Voges_Proskauer_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_complete_annotation.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_grayi_DSM_20601_important_features.dat
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Acetate_utilization_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Alkaline_phosphatase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Arginine_dihydrolase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Bacillus_or_coccobacillus_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Catalase_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Coagulase_production_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_D-Sorbitol_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Esculin_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Facultative_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Glucose_fermenter_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Gram_positive_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_at_42°C_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_in_6.5%_NaCl_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_in_KCN_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Growth_on_ordinary_blood_agar_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Lactose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Malonate_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Maltose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Methyl_red_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Motile_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Salicin_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Starch_hydrolysis_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Trehalose_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_Voges_Proskauer_important_features.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_complete_annotation.gff
traitar/data/sample_data/traitar_out/phenotype_prediction/phypat/feat_gffs/Listeria_ivanovii_WSLC3009_important_features.dat