Merge pull request #1 from ARB-Lab/master

Merge upstream changes in autopacmen to this branch
klamt-lab · Nov 20, 2020 · be1c188 · be1c188
2 parents 786ad0c + 69a1580
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diff --git a/...MATLAB/README_Model_Calibrator_MATLAB.txt → AutoPACMEN_Model_Calibrator_MATLAB/README.md b/...MATLAB/README_Model_Calibrator_MATLAB.txt → AutoPACMEN_Model_Calibrator_MATLAB/README.md
@@ -5,5 +5,5 @@ for an example of the Model Calibrator's kcat optimization method usage.
 NOTE: You have to change the paths to the iJO1366*C model (see Supplementary File 1) to its location on your
 system in order to rerun "kcat_optimization_run_fmincon_ec_model_2019_06_25.m".
 
-MATLAB scripts starting with "p_" are considered "private" scripts which are not intended for a direct
+MATLAB scripts starting with "p_" are considered "private" scripts which are not intended for direct
 usage by the user and are therefore not documented in the manual.
diff --git a/...06_25_manual_changes_change_factor_50.mat → ...06_25_manual_changes_change_factor_50.mat b/...06_25_manual_changes_change_factor_50.mat → ...06_25_manual_changes_change_factor_50.mat
diff --git a/...ization_run_fmincon_ec_model_2019_06_25.m → ...ization_run_fmincon_ec_model_2019_06_25.m b/...ization_run_fmincon_ec_model_2019_06_25.m → ...ization_run_fmincon_ec_model_2019_06_25.m
diff --git a/...brator_MATLAB/optimization_scenarios.json → ...brator_MATLAB/optimization_scenarios.json b/...brator_MATLAB/optimization_scenarios.json → ...brator_MATLAB/optimization_scenarios.json
diff --git a/...brator_MATLAB/p_apply_scenario_on_model.m → ...brator_MATLAB/p_apply_scenario_on_model.m b/...brator_MATLAB/p_apply_scenario_on_model.m → ...brator_MATLAB/p_apply_scenario_on_model.m
diff --git a/..._MATLAB/p_get_objective_value_for_kcats.m → ..._MATLAB/p_get_objective_value_for_kcats.m b/..._MATLAB/p_get_objective_value_for_kcats.m → ..._MATLAB/p_get_objective_value_for_kcats.m
diff --git a/...LAB/p_get_objective_value_for_prot_pool.m → ...LAB/p_get_objective_value_for_prot_pool.m b/...LAB/p_get_objective_value_for_prot_pool.m → ...LAB/p_get_objective_value_for_prot_pool.m
diff --git a/...brator_MATLAB/smoment_kcat_optimization.m → ...brator_MATLAB/smoment_kcat_optimization.m b/...brator_MATLAB/smoment_kcat_optimization.m → ...brator_MATLAB/smoment_kcat_optimization.m
diff --git a/...r_MATLAB/smoment_prot_pool_optimization.m → ...r_MATLAB/smoment_prot_pool_optimization.m b/...r_MATLAB/smoment_prot_pool_optimization.m → ...r_MATLAB/smoment_prot_pool_optimization.m
diff --git a/...06_25_manual_changes_change_factor_50.mat → ...06_25_manual_changes_change_factor_50.mat b/...06_25_manual_changes_change_factor_50.mat → ...06_25_manual_changes_change_factor_50.mat
diff --git a/README.md b/README.md
@@ -6,67 +6,64 @@
 ## General Description
 
 AutoPACMEN allows one to apply the sMOMENT method of automatically expanding a stoichiometric metabolic
-model with protein allocation constraints ([Bekiaris & Klamt, 2020](#autopacmens-publication)).
-AutoPACMEN consists of 2 parts:
-1) A Python 3 Model Generator which primarily uses [cobrapy](https://github.com/opencobra/cobrapy) and which applies the sMOMENT
-   method on a stoichiometric metabolic model.
-2) An optional mixed Python 3/MATLAB Model Calibrator whose MATLAB parts primarily use [CellNetAnalyzer](https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html)
-   and which allows one to optimize given protein allocation constraints in order to get a better fit
-   with <i>in vivo</i> data.
+model with protein allocation constraints (as described in further detail in [Bekiaris & Klamt, 2020](#autopacmens-publication)).
 
+This repository of AutoPACMEN consists of three source code parts:
+
+1) The AutoPACMEN Model Generator, implemented as the Python module "autopacmen-Paulocracy" module, which provides a mostly automated way to generate enzyme-constraint-enhanced stoichiometric metabolic models, including an automatic retrieval of k<sub>cat</sub> values. It is primarily dependent on [cobrapy](https://github.com/opencobra/cobrapy).
+<br>→This module can be found in the "autopacmen" subfolder.
+
+2) An optional mixed Python 3/MATLAB AutoPACMEN Model Calibrator whose MATLAB parts primarily use [CellNetAnalyzer](https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html) and which allows one to optimize given protein allocation constraints in order to get a better fit with <i>in vivo</i> data.
+<br>→The Python parts can be found in the "autopacmen" subfolder as described in AutoPACMEN's manual,the MATLAB parts can be found in the subfolder "AutoPACMEN_Model_Calibrator_MATLAB".
+
+3) The exemplary usage of autopacmen-Paulocracy and the Model Calibrator resulting in the enzyme-constraint-enhanced model iJO1366*, as described in Supplementary File 1 of AutoPACMEN's publication. The final iJO1366* model is stored in a ready-to-use SBML form as "./iJO1366star/ec_model_2019_06_25_output_optimization/iJO1366star.xml".
+<br>→The relevant scripts and data can be found in the "iJO1366" subfolder. <b>Note:</b> As it has a huge file size, the obligatory downloaded complete BRENDA text file brenda_downloads.txt (as described in AutoPACMEN's manual) is not included here. Instead, it can be downloaded from BRENDA's web site.
 
 ## Documentation
 
-AutoPACMEN's manual can be found as "manual.pdf" or "manual.odt" in the "docs" subfolder of the "autopacmen" folder.
+The combined manual for autopacmen-Paulocracy and the Model Calibrator can be found as "manual.pdf" or LibreOffice-compatible "manual.odt" in the "docs" subfolder folder.
 It explains the manual installation process (without pip, see next chapter for the installation with pip) and usage of AutoPACMEN in detail.
 
-An HTML documentation of the source code of AutoPACMEN's Python modules can be found under the main folder's subfolder "html".
+An additional HTML documentation of the source code of AutoPACMEN's Python modules can be found under the "autopacmen" folder's subfolder "html".
 This HTML documentation was automatically generated using [pdoc3](https://pdoc3.github.io/pdoc/) (link accessed on Oct 30, 2019).
-The HTML documentation's starting point is "index.html" in the "./html/autopacmen" subfolder.
-
-In addition, the exemplary usage of AutoPACMEN with iJO1366* is explained in AutoPACMEN's publication Supplementary File 1.
-
-<b>Note:</b> As it has a huge file size, the downloaded complete BRENDA text file brenda_downloads.txt (as described in
-AutoPACMEN's manual) is not included here.
+The HTML documentation's starting point is "index.html" in the "./autopacmen/html/autopacmen" subfolder.
 
 If you are particularily interested in the generation of k<sub>cat</sub> databases from BRENDA and SABIO-RK, look up
 the scripts "data_parse_brenda_textfile.py", "data_parse_sabio_rk_for_model.py" as well as the combining
 script "data_create_combined_kcat_database.py". These scripts create JSON files with the k<sub>cat</sub> data from these
 databases with EC number, organism and substrate information. An exemplary created database with BRENDA is
-"kcat_database_brenda" in the main folder's  subfolder "ec_model_2019_06_25_output", a database with SABIO-RK is
+"kcat_database_brenda" in the main folder's  subfolder "./iJO1366star/ec_model_2019_06_25_output", a database with SABIO-RK is
 "kcat_database_sabio_rk" in the same subfolder.
 
-AutoPACMEN requires Python >=3.7 for its Python parts, and MATLAB >=2017a for its optional Model Calibrator
-MATLAB scripts.
 
+## Installation of autopacmen-Paulocracy using pip
 
-
-## Installation of Python parts using pip
-
-You can install the Python parts of AutoPACMEN's latest release [from PyPI](https://pypi.org/project/autopacmen-Paulocracy/) using pip as follows:
+You can install autopacmen-Paulocracy [from PyPI](https://pypi.org/project/autopacmen-Paulocracy/) using pip as follows:
 <pre>
 pip install autopacmen-Paulocracy
 </pre>
 
+autopacmen-Paulocracy requires Python >=3.7 for its Python parts, and MATLAB >=2017a for its optional Model Calibrator
+MATLAB scripts.
+
 
 ## Structure of AutoPACMEN's source code
 
-<b>All relevant scripts are in the "autopacmen" main folder.</b>
+All relevant scripts of autopacmen-Paulocracy are in the "autopacmen" main folder.
 
 In this main folder, the scripts which start with "analysis_", "data_" and "modeling_" are command-line interfaces (CLI)
 for AutoPACMEN's Python modules. These Python modules can be found the main folder's "submodules" subfolder.
 
-The main folder's subfolder "AutoPACMEN_Model_Calibrator_MATLAB" contains the Model Calibrator's MATLAB parts.
+The subfolder "AutoPACMEN_Model_Calibrator_MATLAB" contains the Model Calibrator's MATLAB parts.
 
-All scripts and folders starting with "ec_model_2019_06_25" are part of the generation and analysis of iJO1366* (see AutoPACMEN's publication for more on it). From these scripts, these ones
-starting with "ec_model_2019_06_25_figure" create either a full figure or data for a figure used in AutoPACMEN's publication.
+All scripts and folders within "iJO1366star" are part of the generation and analysis of iJO1366* (see AutoPACMEN's publication for more about it). From these scripts, these ones
+starting with "./iJO1366star/ec_model_2019_06_25_figure" create either a full figure or data for a figure used in AutoPACMEN's publication.
 
-The main script for the generation of the uncalibrated iJO1366* model is "ec_model_2019_06_25_sMOMENT_iJO_CREATION.py" in the main folder. This
+The main script for the generation of the uncalibrated iJO1366* model is "./iJO1366star/ec_model_2019_06_25_sMOMENT_iJO_CREATION.py" in the "iJO1366" subfolder. This
 main script uses AutoPACMEN's functionalities as Python modules. The commented steps in this script correspond to the steps described in supplementary
 File 1 of (Bekiaris & Klamt, in submission).
 
-
-The main folder's subfolder "iJOstar_MCS_analysis_scripts" contains the scripts used for the computation and the analysis of the published Minimal Cut Set enumeration
+The "iJO1366star" folder's subfolder "iJOstar_MCS_analysis_scripts" contains the scripts used for the computation and the analysis of the published Minimal Cut Set enumeration
 with iJO1366 and iJO1366*.
 
 AutoPACMEN creates a cache of SABIO-RK, NCBI TAXONOMY and UniProt data in the "_cache" main folder's subfolder.  In the current state, the cache is the one

diff --git a/...axonomy/Acanthamoeba castellanii_taxonomy → ...axonomy/Acanthamoeba castellanii_taxonomy b/...axonomy/Acanthamoeba castellanii_taxonomy → ...axonomy/Acanthamoeba castellanii_taxonomy
diff --git a/...Acanthamoeba polyphaga mimivirus_taxonomy → ...Acanthamoeba polyphaga mimivirus_taxonomy b/...Acanthamoeba polyphaga mimivirus_taxonomy → ...Acanthamoeba polyphaga mimivirus_taxonomy
diff --git a/...nomy/Acetoanaerobium sticklandii_taxonomy → ...nomy/Acetoanaerobium sticklandii_taxonomy b/...nomy/Acetoanaerobium sticklandii_taxonomy → ...nomy/Acetoanaerobium sticklandii_taxonomy
diff --git a/.../ncbi_taxonomy/Acetobacter aceti_taxonomy → .../ncbi_taxonomy/Acetobacter aceti_taxonomy b/.../ncbi_taxonomy/Acetobacter aceti_taxonomy → .../ncbi_taxonomy/Acetobacter aceti_taxonomy
diff --git a/..._taxonomy/Acetobacter xylinus_taxonomy_NA → ..._taxonomy/Acetobacter xylinus_taxonomy_NA b/..._taxonomy/Acetobacter xylinus_taxonomy_NA → ..._taxonomy/Acetobacter xylinus_taxonomy_NA
diff --git a/..._cache/ncbi_taxonomy/Acetobacter_taxonomy → _cache/ncbi_taxonomy/Acetobacter_taxonomy b/..._cache/ncbi_taxonomy/Acetobacter_taxonomy → _cache/ncbi_taxonomy/Acetobacter_taxonomy
diff --git a/..._taxonomy/Acholeplasma laidlawii_taxonomy → ..._taxonomy/Acholeplasma laidlawii_taxonomy b/..._taxonomy/Acholeplasma laidlawii_taxonomy → ..._taxonomy/Acholeplasma laidlawii_taxonomy
diff --git a/...ache/ncbi_taxonomy/Acidianus sp._taxonomy → _cache/ncbi_taxonomy/Acidianus sp._taxonomy b/...ache/ncbi_taxonomy/Acidianus sp._taxonomy → _cache/ncbi_taxonomy/Acidianus sp._taxonomy
diff --git a/...xonomy/Acidilobus saccharovorans_taxonomy → ...xonomy/Acidilobus saccharovorans_taxonomy b/...xonomy/Acidilobus saccharovorans_taxonomy → ...xonomy/Acidilobus saccharovorans_taxonomy
diff --git a/...y/Acidithiobacillus ferrooxidans_taxonomy → ...y/Acidithiobacillus ferrooxidans_taxonomy b/...y/Acidithiobacillus ferrooxidans_taxonomy → ...y/Acidithiobacillus ferrooxidans_taxonomy
diff --git a/...taxonomy/Acinetobacter baumannii_taxonomy → ...taxonomy/Acinetobacter baumannii_taxonomy b/...taxonomy/Acinetobacter baumannii_taxonomy → ...taxonomy/Acinetobacter baumannii_taxonomy
diff --git a/...bi_taxonomy/Acinetobacter baylyi_taxonomy → ...bi_taxonomy/Acinetobacter baylyi_taxonomy b/...bi_taxonomy/Acinetobacter baylyi_taxonomy → ...bi_taxonomy/Acinetobacter baylyi_taxonomy
diff --git a/...coaceticus (subsp. anitratus)_taxonomy_NA → ...coaceticus (subsp. anitratus)_taxonomy_NA b/...coaceticus (subsp. anitratus)_taxonomy_NA → ...coaceticus (subsp. anitratus)_taxonomy_NA
diff --git a/...r calcoaceticus subsp. anitratus_taxonomy → ...r calcoaceticus subsp. anitratus_taxonomy b/...r calcoaceticus subsp. anitratus_taxonomy → ...r calcoaceticus subsp. anitratus_taxonomy
diff --git a/...nomy/Acinetobacter calcoaceticus_taxonomy → ...nomy/Acinetobacter calcoaceticus_taxonomy b/...nomy/Acinetobacter calcoaceticus_taxonomy → ...nomy/Acinetobacter calcoaceticus_taxonomy
diff --git a/...cbi_taxonomy/Actinidia chinensis_taxonomy → ...cbi_taxonomy/Actinidia chinensis_taxonomy b/...cbi_taxonomy/Actinidia chinensis_taxonomy → ...cbi_taxonomy/Actinidia chinensis_taxonomy
diff --git a/...bi_taxonomy/Actinomadura sp. R39_taxonomy → ...bi_taxonomy/Actinomadura sp. R39_taxonomy b/...bi_taxonomy/Actinomadura sp. R39_taxonomy → ...bi_taxonomy/Actinomadura sp. R39_taxonomy
diff --git a/...e/ncbi_taxonomy/Actinomadura sp._taxonomy → ...e/ncbi_taxonomy/Actinomadura sp._taxonomy b/...e/ncbi_taxonomy/Actinomadura sp._taxonomy → ...e/ncbi_taxonomy/Actinomadura sp._taxonomy
diff --git a/...onomy/Actinoplanes missouriensis_taxonomy → ...onomy/Actinoplanes missouriensis_taxonomy b/...onomy/Actinoplanes missouriensis_taxonomy → ...onomy/Actinoplanes missouriensis_taxonomy
diff --git a/...nema pretiosum subsp. auranticum_taxonomy → ...nema pretiosum subsp. auranticum_taxonomy b/...nema pretiosum subsp. auranticum_taxonomy → ...nema pretiosum subsp. auranticum_taxonomy
diff --git a/...omy/Advenella mimigardefordensis_taxonomy → ...omy/Advenella mimigardefordensis_taxonomy b/...omy/Advenella mimigardefordensis_taxonomy → ...omy/Advenella mimigardefordensis_taxonomy
diff --git a/...ache/ncbi_taxonomy/Aedes aegypti_taxonomy → _cache/ncbi_taxonomy/Aedes aegypti_taxonomy b/...ache/ncbi_taxonomy/Aedes aegypti_taxonomy → _cache/ncbi_taxonomy/Aedes aegypti_taxonomy
diff --git a/...i_taxonomy/Aeribacillus pallidus_taxonomy → ...i_taxonomy/Aeribacillus pallidus_taxonomy b/...i_taxonomy/Aeribacillus pallidus_taxonomy → ...i_taxonomy/Aeribacillus pallidus_taxonomy
diff --git a/...bi_taxonomy/Aeromonas hydrophila_taxonomy → ...bi_taxonomy/Aeromonas hydrophila_taxonomy b/...bi_taxonomy/Aeromonas hydrophila_taxonomy → ...bi_taxonomy/Aeromonas hydrophila_taxonomy
diff --git a/...cbi_taxonomy/Aeropyrum pernix K1_taxonomy → ...cbi_taxonomy/Aeropyrum pernix K1_taxonomy b/...cbi_taxonomy/Aeropyrum pernix K1_taxonomy → ...cbi_taxonomy/Aeropyrum pernix K1_taxonomy
diff --git a/...e/ncbi_taxonomy/Aeropyrum pernix_taxonomy → ...e/ncbi_taxonomy/Aeropyrum pernix_taxonomy b/...e/ncbi_taxonomy/Aeropyrum pernix_taxonomy → ...e/ncbi_taxonomy/Aeropyrum pernix_taxonomy
diff --git a/.../ncbi_taxonomy/Agaricus bisporus_taxonomy → .../ncbi_taxonomy/Agaricus bisporus_taxonomy b/.../ncbi_taxonomy/Agaricus bisporus_taxonomy → .../ncbi_taxonomy/Agaricus bisporus_taxonomy
diff --git a/...xonomy/Agrobacterium tumefaciens_taxonomy → ...xonomy/Agrobacterium tumefaciens_taxonomy b/...xonomy/Agrobacterium tumefaciens_taxonomy → ...xonomy/Agrobacterium tumefaciens_taxonomy
diff --git a/...bi_taxonomy/Alcaligenes faecalis_taxonomy → ...bi_taxonomy/Alcaligenes faecalis_taxonomy b/...bi_taxonomy/Alcaligenes faecalis_taxonomy → ...bi_taxonomy/Alcaligenes faecalis_taxonomy
diff --git a/...taxonomy/Alcanivorax borkumensis_taxonomy → ...taxonomy/Alcanivorax borkumensis_taxonomy b/...taxonomy/Alcanivorax borkumensis_taxonomy → ...taxonomy/Alcanivorax borkumensis_taxonomy
diff --git a/...ocaldarius subsp. acidocaldarius_taxonomy → ...ocaldarius subsp. acidocaldarius_taxonomy b/...ocaldarius subsp. acidocaldarius_taxonomy → ...ocaldarius subsp. acidocaldarius_taxonomy
diff --git a/.../Alicyclobacillus acidocaldarius_taxonomy → .../Alicyclobacillus acidocaldarius_taxonomy b/.../Alicyclobacillus acidocaldarius_taxonomy → .../Alicyclobacillus acidocaldarius_taxonomy
diff --git a/...taxonomy/Alkaliphilus oremlandii_taxonomy → ...taxonomy/Alkaliphilus oremlandii_taxonomy b/...taxonomy/Alkaliphilus oremlandii_taxonomy → ...taxonomy/Alkaliphilus oremlandii_taxonomy
diff --git a/...onomy/Alligator mississippiensis_taxonomy → ...onomy/Alligator mississippiensis_taxonomy b/...onomy/Alligator mississippiensis_taxonomy → ...onomy/Alligator mississippiensis_taxonomy
diff --git a/..._taxonomy/Allochromatium vinosum_taxonomy → ..._taxonomy/Allochromatium vinosum_taxonomy b/..._taxonomy/Allochromatium vinosum_taxonomy → ..._taxonomy/Allochromatium vinosum_taxonomy
diff --git a/...he/ncbi_taxonomy/Alnus glutinosa_taxonomy → ...he/ncbi_taxonomy/Alnus glutinosa_taxonomy b/...he/ncbi_taxonomy/Alnus glutinosa_taxonomy → ...he/ncbi_taxonomy/Alnus glutinosa_taxonomy
diff --git a/..._taxonomy/Alternanthera ficoidea_taxonomy → ..._taxonomy/Alternanthera ficoidea_taxonomy b/..._taxonomy/Alternanthera ficoidea_taxonomy → ..._taxonomy/Alternanthera ficoidea_taxonomy
diff --git a/...i_taxonomy/Alternanthera pungens_taxonomy → ...i_taxonomy/Alternanthera pungens_taxonomy b/...i_taxonomy/Alternanthera pungens_taxonomy → ...i_taxonomy/Alternanthera pungens_taxonomy
diff --git a/..._taxonomy/Alternanthera sessilis_taxonomy → ..._taxonomy/Alternanthera sessilis_taxonomy b/..._taxonomy/Alternanthera sessilis_taxonomy → ..._taxonomy/Alternanthera sessilis_taxonomy
diff --git a/...i_taxonomy/Alteromonas macleodii_taxonomy → ...i_taxonomy/Alteromonas macleodii_taxonomy b/...i_taxonomy/Alteromonas macleodii_taxonomy → ...i_taxonomy/Alteromonas macleodii_taxonomy
diff --git a/...he/ncbi_taxonomy/Alteromonas sp._taxonomy → ...he/ncbi_taxonomy/Alteromonas sp._taxonomy b/...he/ncbi_taxonomy/Alteromonas sp._taxonomy → ...he/ncbi_taxonomy/Alteromonas sp._taxonomy
diff --git a/...axonomy/Amycolatopsis orientalis_taxonomy → ...axonomy/Amycolatopsis orientalis_taxonomy b/...axonomy/Amycolatopsis orientalis_taxonomy → ...axonomy/Amycolatopsis orientalis_taxonomy
diff --git a/.../ncbi_taxonomy/Amycolatopsis sp._taxonomy → .../ncbi_taxonomy/Amycolatopsis sp._taxonomy b/.../ncbi_taxonomy/Amycolatopsis sp._taxonomy → .../ncbi_taxonomy/Amycolatopsis sp._taxonomy
diff --git a/...cbi_taxonomy/Anabaena azollae_taxonomy_NA → ...cbi_taxonomy/Anabaena azollae_taxonomy_NA b/...cbi_taxonomy/Anabaena azollae_taxonomy_NA → ...cbi_taxonomy/Anabaena azollae_taxonomy_NA
diff --git a/...cache/ncbi_taxonomy/Anabaena sp._taxonomy → _cache/ncbi_taxonomy/Anabaena sp._taxonomy b/...cache/ncbi_taxonomy/Anabaena sp._taxonomy → _cache/ncbi_taxonomy/Anabaena sp._taxonomy
diff --git a/...obiospirillum succiniciproducens_taxonomy → ...obiospirillum succiniciproducens_taxonomy b/...obiospirillum succiniciproducens_taxonomy → ...obiospirillum succiniciproducens_taxonomy
diff --git a/...axonomy/Anaerotignum propionicum_taxonomy → ...axonomy/Anaerotignum propionicum_taxonomy b/...axonomy/Anaerotignum propionicum_taxonomy → ...axonomy/Anaerotignum propionicum_taxonomy
diff --git a/...ncbi_taxonomy/Anas platyrhynchos_taxonomy → ...ncbi_taxonomy/Anas platyrhynchos_taxonomy b/...ncbi_taxonomy/Anas platyrhynchos_taxonomy → ...ncbi_taxonomy/Anas platyrhynchos_taxonomy
diff --git a/.../ncbi_taxonomy/Anguilla anguilla_taxonomy → .../ncbi_taxonomy/Anguilla anguilla_taxonomy b/.../ncbi_taxonomy/Anguilla anguilla_taxonomy → .../ncbi_taxonomy/Anguilla anguilla_taxonomy
diff --git a/.../ncbi_taxonomy/Anopheles gambiae_taxonomy → .../ncbi_taxonomy/Anopheles gambiae_taxonomy b/.../ncbi_taxonomy/Anopheles gambiae_taxonomy → .../ncbi_taxonomy/Anopheles gambiae_taxonomy
diff --git a/...onomy/Anoxybacillus flavithermus_taxonomy → ...onomy/Anoxybacillus flavithermus_taxonomy b/...onomy/Anoxybacillus flavithermus_taxonomy → ...onomy/Anoxybacillus flavithermus_taxonomy
diff --git a/..._taxonomy/Anoxybacillus gonensis_taxonomy → ..._taxonomy/Anoxybacillus gonensis_taxonomy b/..._taxonomy/Anoxybacillus gonensis_taxonomy → ..._taxonomy/Anoxybacillus gonensis_taxonomy
diff --git a/...n/_cache/ncbi_taxonomy/Anser sp._taxonomy → _cache/ncbi_taxonomy/Anser sp._taxonomy b/...n/_cache/ncbi_taxonomy/Anser sp._taxonomy → _cache/ncbi_taxonomy/Anser sp._taxonomy
diff --git a/...axonomy/Antarctic bacterium TAB5_taxonomy → ...axonomy/Antarctic bacterium TAB5_taxonomy b/...axonomy/Antarctic bacterium TAB5_taxonomy → ...axonomy/Antarctic bacterium TAB5_taxonomy
diff --git a/...ncbi_taxonomy/Apis cerana indica_taxonomy → ...ncbi_taxonomy/Apis cerana indica_taxonomy b/...ncbi_taxonomy/Apis cerana indica_taxonomy → ...ncbi_taxonomy/Apis cerana indica_taxonomy
diff --git a/...bi_taxonomy/Apis cerana japonica_taxonomy → ...bi_taxonomy/Apis cerana japonica_taxonomy b/...bi_taxonomy/Apis cerana japonica_taxonomy → ...bi_taxonomy/Apis cerana japonica_taxonomy
diff --git a/...che/ncbi_taxonomy/Apis mellifera_taxonomy → _cache/ncbi_taxonomy/Apis mellifera_taxonomy b/...che/ncbi_taxonomy/Apis mellifera_taxonomy → _cache/ncbi_taxonomy/Apis mellifera_taxonomy
diff --git a/...cbi_taxonomy/Aplysia californica_taxonomy → ...cbi_taxonomy/Aplysia californica_taxonomy b/...cbi_taxonomy/Aplysia californica_taxonomy → ...cbi_taxonomy/Aplysia californica_taxonomy
diff --git a/...e/ncbi_taxonomy/Aplysia fasciata_taxonomy → ...e/ncbi_taxonomy/Aplysia fasciata_taxonomy b/...e/ncbi_taxonomy/Aplysia fasciata_taxonomy → ...e/ncbi_taxonomy/Aplysia fasciata_taxonomy
diff --git a/..._taxonomy/Aquaspirillum arcticum_taxonomy → ..._taxonomy/Aquaspirillum arcticum_taxonomy b/..._taxonomy/Aquaspirillum arcticum_taxonomy → ..._taxonomy/Aquaspirillum arcticum_taxonomy
diff --git a/...e/ncbi_taxonomy/Aquifex aeolicus_taxonomy → ...e/ncbi_taxonomy/Aquifex aeolicus_taxonomy b/...e/ncbi_taxonomy/Aquifex aeolicus_taxonomy → ...e/ncbi_taxonomy/Aquifex aeolicus_taxonomy
diff --git a/...ncbi_taxonomy/Aquifex pyrophilus_taxonomy → ...ncbi_taxonomy/Aquifex pyrophilus_taxonomy b/...ncbi_taxonomy/Aquifex pyrophilus_taxonomy → ...ncbi_taxonomy/Aquifex pyrophilus_taxonomy
diff --git a/...bi_taxonomy/Arabidopsis thaliana_taxonomy → ...bi_taxonomy/Arabidopsis thaliana_taxonomy b/...bi_taxonomy/Arabidopsis thaliana_taxonomy → ...bi_taxonomy/Arabidopsis thaliana_taxonomy
diff --git a/..._taxonomy/Archaeoglobus fulgidus_taxonomy → ..._taxonomy/Archaeoglobus fulgidus_taxonomy b/..._taxonomy/Archaeoglobus fulgidus_taxonomy → ..._taxonomy/Archaeoglobus fulgidus_taxonomy
diff --git a/..._taxonomy/Aromatoleum aromaticum_taxonomy → ..._taxonomy/Aromatoleum aromaticum_taxonomy b/..._taxonomy/Aromatoleum aromaticum_taxonomy → ..._taxonomy/Aromatoleum aromaticum_taxonomy
diff --git a/...i_taxonomy/Artemisia spiciformis_taxonomy → ...i_taxonomy/Artemisia spiciformis_taxonomy b/...i_taxonomy/Artemisia spiciformis_taxonomy → ...i_taxonomy/Artemisia spiciformis_taxonomy
diff --git a/...tridentata subsp. spiciformis_taxonomy_NA → ...tridentata subsp. spiciformis_taxonomy_NA b/...tridentata subsp. spiciformis_taxonomy_NA → ...tridentata subsp. spiciformis_taxonomy_NA
diff --git a/...axonomy/Arthrobacter globiformis_taxonomy → ...axonomy/Arthrobacter globiformis_taxonomy b/...axonomy/Arthrobacter globiformis_taxonomy → ...axonomy/Arthrobacter globiformis_taxonomy
diff --git a/...y/Arthrobacter nicotinovorans_taxonomy_NA → ...y/Arthrobacter nicotinovorans_taxonomy_NA b/...y/Arthrobacter nicotinovorans_taxonomy_NA → ...y/Arthrobacter nicotinovorans_taxonomy_NA
diff --git a/.../Arthrobacter psychrolactophilus_taxonomy → .../Arthrobacter psychrolactophilus_taxonomy b/.../Arthrobacter psychrolactophilus_taxonomy → .../Arthrobacter psychrolactophilus_taxonomy
diff --git a/...e/ncbi_taxonomy/Arthrobacter sp._taxonomy → ...e/ncbi_taxonomy/Arthrobacter sp._taxonomy b/...e/ncbi_taxonomy/Arthrobacter sp._taxonomy → ...e/ncbi_taxonomy/Arthrobacter sp._taxonomy
diff --git a/...cache/ncbi_taxonomy/Ascaris suum_taxonomy → _cache/ncbi_taxonomy/Ascaris suum_taxonomy b/...cache/ncbi_taxonomy/Ascaris suum_taxonomy → _cache/ncbi_taxonomy/Ascaris suum_taxonomy
diff --git a/...i_taxonomy/Aspergillus aculeatus_taxonomy → ...i_taxonomy/Aspergillus aculeatus_taxonomy b/...i_taxonomy/Aspergillus aculeatus_taxonomy → ...i_taxonomy/Aspergillus aculeatus_taxonomy
diff --git a/...taxonomy/Aspergillus carbonarius_taxonomy → ...taxonomy/Aspergillus carbonarius_taxonomy b/...taxonomy/Aspergillus carbonarius_taxonomy → ...taxonomy/Aspergillus carbonarius_taxonomy
diff --git a/...bi_taxonomy/Aspergillus clavatus_taxonomy → ...bi_taxonomy/Aspergillus clavatus_taxonomy b/...bi_taxonomy/Aspergillus clavatus_taxonomy → ...bi_taxonomy/Aspergillus clavatus_taxonomy
diff --git a/...ncbi_taxonomy/Aspergillus flavus_taxonomy → ...ncbi_taxonomy/Aspergillus flavus_taxonomy b/...ncbi_taxonomy/Aspergillus flavus_taxonomy → ...ncbi_taxonomy/Aspergillus flavus_taxonomy
diff --git a/...i_taxonomy/Aspergillus fumigatus_taxonomy → ...i_taxonomy/Aspergillus fumigatus_taxonomy b/...i_taxonomy/Aspergillus fumigatus_taxonomy → ...i_taxonomy/Aspergillus fumigatus_taxonomy
diff --git a/...bi_taxonomy/Aspergillus nidulans_taxonomy → ...bi_taxonomy/Aspergillus nidulans_taxonomy b/...bi_taxonomy/Aspergillus nidulans_taxonomy → ...bi_taxonomy/Aspergillus nidulans_taxonomy
diff --git a/.../ncbi_taxonomy/Aspergillus niger_taxonomy → .../ncbi_taxonomy/Aspergillus niger_taxonomy b/.../ncbi_taxonomy/Aspergillus niger_taxonomy → .../ncbi_taxonomy/Aspergillus niger_taxonomy
diff --git a/...ncbi_taxonomy/Aspergillus niveus_taxonomy → ...ncbi_taxonomy/Aspergillus niveus_taxonomy b/...ncbi_taxonomy/Aspergillus niveus_taxonomy → ...ncbi_taxonomy/Aspergillus niveus_taxonomy
diff --git a/...ncbi_taxonomy/Aspergillus oryzae_taxonomy → ...ncbi_taxonomy/Aspergillus oryzae_taxonomy b/...ncbi_taxonomy/Aspergillus oryzae_taxonomy → ...ncbi_taxonomy/Aspergillus oryzae_taxonomy
diff --git a/.../ncbi_taxonomy/Aspergillus sojae_taxonomy → .../ncbi_taxonomy/Aspergillus sojae_taxonomy b/.../ncbi_taxonomy/Aspergillus sojae_taxonomy → .../ncbi_taxonomy/Aspergillus sojae_taxonomy
diff --git a/...i_taxonomy/Astrosclera willeyana_taxonomy → ...i_taxonomy/Astrosclera willeyana_taxonomy b/...i_taxonomy/Astrosclera willeyana_taxonomy → ...i_taxonomy/Astrosclera willeyana_taxonomy
diff --git a/...ca multiple nucleopolyhedrovirus_taxonomy → ...ca multiple nucleopolyhedrovirus_taxonomy b/...ca multiple nucleopolyhedrovirus_taxonomy → ...ca multiple nucleopolyhedrovirus_taxonomy
diff --git a/...cache/ncbi_taxonomy/Avena sativa_taxonomy → _cache/ncbi_taxonomy/Avena sativa_taxonomy b/...cache/ncbi_taxonomy/Avena sativa_taxonomy → _cache/ncbi_taxonomy/Avena sativa_taxonomy
diff --git a/...e/ncbi_taxonomy/Avicennia marina_taxonomy → ...e/ncbi_taxonomy/Avicennia marina_taxonomy b/...e/ncbi_taxonomy/Avicennia marina_taxonomy → ...e/ncbi_taxonomy/Avicennia marina_taxonomy
diff --git a/...e/ncbi_taxonomy/Azoarcus evansii_taxonomy → ...e/ncbi_taxonomy/Azoarcus evansii_taxonomy b/...e/ncbi_taxonomy/Azoarcus evansii_taxonomy → ...e/ncbi_taxonomy/Azoarcus evansii_taxonomy
diff --git a/...taxonomy/Azospirillum brasilense_taxonomy → ...taxonomy/Azospirillum brasilense_taxonomy b/...taxonomy/Azospirillum brasilense_taxonomy → ...taxonomy/Azospirillum brasilense_taxonomy
diff --git a/...taxonomy/Azotobacter chroococcum_taxonomy → ...taxonomy/Azotobacter chroococcum_taxonomy b/...taxonomy/Azotobacter chroococcum_taxonomy → ...taxonomy/Azotobacter chroococcum_taxonomy
diff --git a/..._taxonomy/Azotobacter vinelandii_taxonomy → ..._taxonomy/Azotobacter vinelandii_taxonomy b/..._taxonomy/Azotobacter vinelandii_taxonomy → ..._taxonomy/Azotobacter vinelandii_taxonomy
diff --git a/...ache/ncbi_taxonomy/Babesia bovis_taxonomy → _cache/ncbi_taxonomy/Babesia bovis_taxonomy b/...ache/ncbi_taxonomy/Babesia bovis_taxonomy → _cache/ncbi_taxonomy/Babesia bovis_taxonomy
diff --git a/...he/ncbi_taxonomy/Babesia gibsoni_taxonomy → ...he/ncbi_taxonomy/Babesia gibsoni_taxonomy b/...he/ncbi_taxonomy/Babesia gibsoni_taxonomy → ...he/ncbi_taxonomy/Babesia gibsoni_taxonomy
diff --git a/...onomy/Bacillus amyloliquefaciens_taxonomy → ...onomy/Bacillus amyloliquefaciens_taxonomy b/...onomy/Bacillus amyloliquefaciens_taxonomy → ...onomy/Bacillus amyloliquefaciens_taxonomy
diff --git a/...ncbi_taxonomy/Bacillus anthracis_taxonomy → ...ncbi_taxonomy/Bacillus anthracis_taxonomy b/...ncbi_taxonomy/Bacillus anthracis_taxonomy → ...ncbi_taxonomy/Bacillus anthracis_taxonomy
diff --git a/..._taxonomy/Bacillus caldotenax_taxonomy_NA → ..._taxonomy/Bacillus caldotenax_taxonomy_NA b/..._taxonomy/Bacillus caldotenax_taxonomy_NA → ..._taxonomy/Bacillus caldotenax_taxonomy_NA
diff --git a/...he/ncbi_taxonomy/Bacillus cereus_taxonomy → ...he/ncbi_taxonomy/Bacillus cereus_taxonomy b/...he/ncbi_taxonomy/Bacillus cereus_taxonomy → ...he/ncbi_taxonomy/Bacillus cereus_taxonomy
diff --git a/...ncbi_taxonomy/Bacillus circulans_taxonomy → ...ncbi_taxonomy/Bacillus circulans_taxonomy b/...ncbi_taxonomy/Bacillus circulans_taxonomy → ...ncbi_taxonomy/Bacillus circulans_taxonomy
diff --git a/...ncbi_taxonomy/Bacillus coagulans_taxonomy → ...ncbi_taxonomy/Bacillus coagulans_taxonomy b/...ncbi_taxonomy/Bacillus coagulans_taxonomy → ...ncbi_taxonomy/Bacillus coagulans_taxonomy
diff --git a/...he/ncbi_taxonomy/Bacillus firmus_taxonomy → ...he/ncbi_taxonomy/Bacillus firmus_taxonomy b/...he/ncbi_taxonomy/Bacillus firmus_taxonomy → ...he/ncbi_taxonomy/Bacillus firmus_taxonomy
diff --git a/...cbi_taxonomy/Bacillus halodurans_taxonomy → ...cbi_taxonomy/Bacillus halodurans_taxonomy b/...cbi_taxonomy/Bacillus halodurans_taxonomy → ...cbi_taxonomy/Bacillus halodurans_taxonomy
diff --git a/..._taxonomy/Bacillus licheniformis_taxonomy → ..._taxonomy/Bacillus licheniformis_taxonomy b/..._taxonomy/Bacillus licheniformis_taxonomy → ..._taxonomy/Bacillus licheniformis_taxonomy
diff --git a/...i_taxonomy/Bacillus methanolicus_taxonomy → ...i_taxonomy/Bacillus methanolicus_taxonomy b/...i_taxonomy/Bacillus methanolicus_taxonomy → ...i_taxonomy/Bacillus methanolicus_taxonomy
diff --git a/...e/ncbi_taxonomy/Bacillus pumilus_taxonomy → ...e/ncbi_taxonomy/Bacillus pumilus_taxonomy b/...e/ncbi_taxonomy/Bacillus pumilus_taxonomy → ...e/ncbi_taxonomy/Bacillus pumilus_taxonomy
diff --git a/...nomy/Bacillus sp. (in: Bacteria)_taxonomy → ...nomy/Bacillus sp. (in: Bacteria)_taxonomy b/...nomy/Bacillus sp. (in: Bacteria)_taxonomy → ...nomy/Bacillus sp. (in: Bacteria)_taxonomy
diff --git a/...e/ncbi_taxonomy/Bacillus sp. PS3_taxonomy → ...e/ncbi_taxonomy/Bacillus sp. PS3_taxonomy b/...e/ncbi_taxonomy/Bacillus sp. PS3_taxonomy → ...e/ncbi_taxonomy/Bacillus sp. PS3_taxonomy
diff --git a/...cbi_taxonomy/Bacillus sp. YM55-1_taxonomy → ...cbi_taxonomy/Bacillus sp. YM55-1_taxonomy b/...cbi_taxonomy/Bacillus sp. YM55-1_taxonomy → ...cbi_taxonomy/Bacillus sp. YM55-1_taxonomy
diff --git a/...he/ncbi_taxonomy/Bacillus sp._taxonomy_NA → ...he/ncbi_taxonomy/Bacillus sp._taxonomy_NA b/...he/ncbi_taxonomy/Bacillus sp._taxonomy_NA → ...he/ncbi_taxonomy/Bacillus sp._taxonomy_NA
diff --git a/.../ncbi_taxonomy/Bacillus subtilis_taxonomy → .../ncbi_taxonomy/Bacillus subtilis_taxonomy b/.../ncbi_taxonomy/Bacillus subtilis_taxonomy → .../ncbi_taxonomy/Bacillus subtilis_taxonomy
diff --git a/..._taxonomy/Bacillus thuringiensis_taxonomy → ..._taxonomy/Bacillus thuringiensis_taxonomy b/..._taxonomy/Bacillus thuringiensis_taxonomy → ..._taxonomy/Bacillus thuringiensis_taxonomy
diff --git a/...i_taxonomy/Bacillus virus SPbeta_taxonomy → ...i_taxonomy/Bacillus virus SPbeta_taxonomy b/...i_taxonomy/Bacillus virus SPbeta_taxonomy → ...i_taxonomy/Bacillus virus SPbeta_taxonomy
diff --git a/...he/ncbi_taxonomy/Bacopa monnieri_taxonomy → ...he/ncbi_taxonomy/Bacopa monnieri_taxonomy b/...he/ncbi_taxonomy/Bacopa monnieri_taxonomy → ...he/ncbi_taxonomy/Bacopa monnieri_taxonomy
diff --git a/...y/Bacteria Latreille et al. 1825_taxonomy → ...y/Bacteria Latreille et al. 1825_taxonomy b/...y/Bacteria Latreille et al. 1825_taxonomy → ...y/Bacteria Latreille et al. 1825_taxonomy
diff --git a/...en/_cache/ncbi_taxonomy/Bacteria_taxonomy → _cache/ncbi_taxonomy/Bacteria_taxonomy b/...en/_cache/ncbi_taxonomy/Bacteria_taxonomy → _cache/ncbi_taxonomy/Bacteria_taxonomy
diff --git a/...cbi_taxonomy/Bacteriophage T4_taxonomy_NA → ...cbi_taxonomy/Bacteriophage T4_taxonomy_NA b/...cbi_taxonomy/Bacteriophage T4_taxonomy_NA → ...cbi_taxonomy/Bacteriophage T4_taxonomy_NA
diff --git a/...taxonomy/Bacteriophage phi-13_taxonomy_NA → ...taxonomy/Bacteriophage phi-13_taxonomy_NA b/...taxonomy/Bacteriophage phi-13_taxonomy_NA → ...taxonomy/Bacteriophage phi-13_taxonomy_NA
diff --git a/..._taxonomy/Bacteriophage phi-6_taxonomy_NA → ..._taxonomy/Bacteriophage phi-6_taxonomy_NA b/..._taxonomy/Bacteriophage phi-6_taxonomy_NA → ..._taxonomy/Bacteriophage phi-6_taxonomy_NA
diff --git a/..._taxonomy/Bacteriophage phi-8_taxonomy_NA → ..._taxonomy/Bacteriophage phi-8_taxonomy_NA b/..._taxonomy/Bacteriophage phi-8_taxonomy_NA → ..._taxonomy/Bacteriophage phi-8_taxonomy_NA
diff --git a/...bi_taxonomy/Bacteroides fragilis_taxonomy → ...bi_taxonomy/Bacteroides fragilis_taxonomy b/...bi_taxonomy/Bacteroides fragilis_taxonomy → ...bi_taxonomy/Bacteroides fragilis_taxonomy
diff --git a/...ncbi_taxonomy/Bacteroides ovatus_taxonomy → ...ncbi_taxonomy/Bacteroides ovatus_taxonomy b/...ncbi_taxonomy/Bacteroides ovatus_taxonomy → ...ncbi_taxonomy/Bacteroides ovatus_taxonomy
diff --git a/...omy/Bacteroides thetaiotaomicron_taxonomy → ...omy/Bacteroides thetaiotaomicron_taxonomy b/...omy/Bacteroides thetaiotaomicron_taxonomy → ...omy/Bacteroides thetaiotaomicron_taxonomy
diff --git a/...e/ncbi_taxonomy/Bambusa oldhamii_taxonomy → ...e/ncbi_taxonomy/Bambusa oldhamii_taxonomy b/...e/ncbi_taxonomy/Bambusa oldhamii_taxonomy → ...e/ncbi_taxonomy/Bambusa oldhamii_taxonomy
diff --git a/...onomy/Bdellovibrio bacteriovorus_taxonomy → ...onomy/Bdellovibrio bacteriovorus_taxonomy b/...onomy/Bdellovibrio bacteriovorus_taxonomy → ...onomy/Bdellovibrio bacteriovorus_taxonomy
diff --git a/...omy/Bifidobacterium adolescentis_taxonomy → ...omy/Bifidobacterium adolescentis_taxonomy b/...omy/Bifidobacterium adolescentis_taxonomy → ...omy/Bifidobacterium adolescentis_taxonomy
diff --git a/...bacterium longum subsp. infantis_taxonomy → ...bacterium longum subsp. infantis_taxonomy b/...bacterium longum subsp. infantis_taxonomy → ...bacterium longum subsp. infantis_taxonomy
diff --git a/...ncbi_taxonomy/Bjerkandera adusta_taxonomy → ...ncbi_taxonomy/Bjerkandera adusta_taxonomy b/...ncbi_taxonomy/Bjerkandera adusta_taxonomy → ...ncbi_taxonomy/Bjerkandera adusta_taxonomy
diff --git a/...ncbi_taxonomy/Bjerkandera fumosa_taxonomy → ...ncbi_taxonomy/Bjerkandera fumosa_taxonomy b/...ncbi_taxonomy/Bjerkandera fumosa_taxonomy → ...ncbi_taxonomy/Bjerkandera fumosa_taxonomy
diff --git a/...he/ncbi_taxonomy/Bjerkandera sp._taxonomy → ...he/ncbi_taxonomy/Bjerkandera sp._taxonomy b/...he/ncbi_taxonomy/Bjerkandera sp._taxonomy → ...he/ncbi_taxonomy/Bjerkandera sp._taxonomy
diff --git a/...onomy/Blastobotrys adeninivorans_taxonomy → ...onomy/Blastobotrys adeninivorans_taxonomy b/...onomy/Blastobotrys adeninivorans_taxonomy → ...onomy/Blastobotrys adeninivorans_taxonomy
diff --git a/...i_taxonomy/Blastochloris viridis_taxonomy → ...i_taxonomy/Blastochloris viridis_taxonomy b/...i_taxonomy/Blastochloris viridis_taxonomy → ...i_taxonomy/Blastochloris viridis_taxonomy
diff --git a/..._cache/ncbi_taxonomy/Bombyx mori_taxonomy → _cache/ncbi_taxonomy/Bombyx mori_taxonomy b/..._cache/ncbi_taxonomy/Bombyx mori_taxonomy → _cache/ncbi_taxonomy/Bombyx mori_taxonomy
diff --git a/...bi_taxonomy/Bordetella pertussis_taxonomy → ...bi_taxonomy/Bordetella pertussis_taxonomy b/...bi_taxonomy/Bordetella pertussis_taxonomy → ...bi_taxonomy/Bordetella pertussis_taxonomy
diff --git a/...taxonomy/Borrelia burgdorferi_taxonomy_NA → ...taxonomy/Borrelia burgdorferi_taxonomy_NA b/...taxonomy/Borrelia burgdorferi_taxonomy_NA → ...taxonomy/Borrelia burgdorferi_taxonomy_NA
diff --git a/...taxonomy/Borreliella burgdorferi_taxonomy → ...taxonomy/Borreliella burgdorferi_taxonomy b/...taxonomy/Borreliella burgdorferi_taxonomy → ...taxonomy/Borreliella burgdorferi_taxonomy
diff --git a/.../_cache/ncbi_taxonomy/Bos taurus_taxonomy → _cache/ncbi_taxonomy/Bos taurus_taxonomy b/.../_cache/ncbi_taxonomy/Bos taurus_taxonomy → _cache/ncbi_taxonomy/Bos taurus_taxonomy
diff --git a/.../ncbi_taxonomy/Bothrops jararaca_taxonomy → .../ncbi_taxonomy/Bothrops jararaca_taxonomy b/.../ncbi_taxonomy/Bothrops jararaca_taxonomy → .../ncbi_taxonomy/Bothrops jararaca_taxonomy
diff --git a/...bi_taxonomy/Botryococcus braunii_taxonomy → ...bi_taxonomy/Botryococcus braunii_taxonomy b/...bi_taxonomy/Botryococcus braunii_taxonomy → ...bi_taxonomy/Botryococcus braunii_taxonomy
diff --git a/...my/Bradyrhizobium diazoefficiens_taxonomy → ...my/Bradyrhizobium diazoefficiens_taxonomy b/...my/Bradyrhizobium diazoefficiens_taxonomy → ...my/Bradyrhizobium diazoefficiens_taxonomy
diff --git a/...axonomy/Bradyrhizobium japonicum_taxonomy → ...axonomy/Bradyrhizobium japonicum_taxonomy b/...axonomy/Bradyrhizobium japonicum_taxonomy → ...axonomy/Bradyrhizobium japonicum_taxonomy
diff --git a/..._taxonomy/Branchiostoma floridae_taxonomy → ..._taxonomy/Branchiostoma floridae_taxonomy b/..._taxonomy/Branchiostoma floridae_taxonomy → ..._taxonomy/Branchiostoma floridae_taxonomy
diff --git a/...xonomy/Branchiostoma lanceolatum_taxonomy → ...xonomy/Branchiostoma lanceolatum_taxonomy b/...xonomy/Branchiostoma lanceolatum_taxonomy → ...xonomy/Branchiostoma lanceolatum_taxonomy
diff --git a/...bi_taxonomy/Brassica capitata_taxonomy_NA → ...bi_taxonomy/Brassica capitata_taxonomy_NA b/...bi_taxonomy/Brassica capitata_taxonomy_NA → ...bi_taxonomy/Brassica capitata_taxonomy_NA
diff --git a/.../ncbi_taxonomy/Brassica oleracea_taxonomy → .../ncbi_taxonomy/Brassica oleracea_taxonomy b/.../ncbi_taxonomy/Brassica oleracea_taxonomy → .../ncbi_taxonomy/Brassica oleracea_taxonomy
diff --git a/...ache/ncbi_taxonomy/Brassica rapa_taxonomy → _cache/ncbi_taxonomy/Brassica rapa_taxonomy b/...ache/ncbi_taxonomy/Brassica rapa_taxonomy → _cache/ncbi_taxonomy/Brassica rapa_taxonomy
diff --git a/...e/ncbi_taxonomy/Brucella abortus_taxonomy → ...e/ncbi_taxonomy/Brucella abortus_taxonomy b/...e/ncbi_taxonomy/Brucella abortus_taxonomy → ...e/ncbi_taxonomy/Brucella abortus_taxonomy
diff --git a/...cbi_taxonomy/Brucella melitensis_taxonomy → ...cbi_taxonomy/Brucella melitensis_taxonomy b/...cbi_taxonomy/Brucella melitensis_taxonomy → ...cbi_taxonomy/Brucella melitensis_taxonomy
diff --git a/...ache/ncbi_taxonomy/Brucella suis_taxonomy → _cache/ncbi_taxonomy/Brucella suis_taxonomy b/...ache/ncbi_taxonomy/Brucella suis_taxonomy → _cache/ncbi_taxonomy/Brucella suis_taxonomy
diff --git a/...ache/ncbi_taxonomy/Brugia malayi_taxonomy → _cache/ncbi_taxonomy/Brugia malayi_taxonomy b/...ache/ncbi_taxonomy/Brugia malayi_taxonomy → _cache/ncbi_taxonomy/Brugia malayi_taxonomy
diff --git a/...he/ncbi_taxonomy/Bubalus bubalis_taxonomy → ...he/ncbi_taxonomy/Bubalus bubalis_taxonomy b/...he/ncbi_taxonomy/Bubalus bubalis_taxonomy → ...he/ncbi_taxonomy/Bubalus bubalis_taxonomy
diff --git a/..._taxonomy/Buckleyzyma aurantiaca_taxonomy → ..._taxonomy/Buckleyzyma aurantiaca_taxonomy b/..._taxonomy/Buckleyzyma aurantiaca_taxonomy → ..._taxonomy/Buckleyzyma aurantiaca_taxonomy
diff --git a/...y/Burkholderia cenocepacia J2315_taxonomy → ...y/Burkholderia cenocepacia J2315_taxonomy b/...y/Burkholderia cenocepacia J2315_taxonomy → ...y/Burkholderia cenocepacia J2315_taxonomy
diff --git a/...axonomy/Burkholderia cenocepacia_taxonomy → ...axonomy/Burkholderia cenocepacia_taxonomy b/...axonomy/Burkholderia cenocepacia_taxonomy → ...axonomy/Burkholderia cenocepacia_taxonomy
diff --git a/...bi_taxonomy/Burkholderia cepacia_taxonomy → ...bi_taxonomy/Burkholderia cepacia_taxonomy b/...bi_taxonomy/Burkholderia cepacia_taxonomy → ...bi_taxonomy/Burkholderia cepacia_taxonomy
diff --git a/...cbi_taxonomy/Burkholderia glumae_taxonomy → ...cbi_taxonomy/Burkholderia glumae_taxonomy b/...cbi_taxonomy/Burkholderia glumae_taxonomy → ...cbi_taxonomy/Burkholderia glumae_taxonomy
diff --git a/...cbi_taxonomy/Burkholderia mallei_taxonomy → ...cbi_taxonomy/Burkholderia mallei_taxonomy b/...cbi_taxonomy/Burkholderia mallei_taxonomy → ...cbi_taxonomy/Burkholderia mallei_taxonomy
diff --git a/...xonomy/Burkholderia pseudomallei_taxonomy → ...xonomy/Burkholderia pseudomallei_taxonomy b/...xonomy/Burkholderia pseudomallei_taxonomy → ...xonomy/Burkholderia pseudomallei_taxonomy
diff --git a/...e/ncbi_taxonomy/Burkholderia sp._taxonomy → ...e/ncbi_taxonomy/Burkholderia sp._taxonomy b/...e/ncbi_taxonomy/Burkholderia sp._taxonomy → ...e/ncbi_taxonomy/Burkholderia sp._taxonomy
diff --git a/...onomy/Burkholderia thailandensis_taxonomy → ...onomy/Burkholderia thailandensis_taxonomy b/...onomy/Burkholderia thailandensis_taxonomy → ...onomy/Burkholderia thailandensis_taxonomy
diff --git a/...Burkholderia xenovorans LB400_taxonomy_NA → ...Burkholderia xenovorans LB400_taxonomy_NA b/...Burkholderia xenovorans LB400_taxonomy_NA → ...Burkholderia xenovorans LB400_taxonomy_NA
diff --git a/...onomy/Burkholderia xenovorans_taxonomy_NA → ...onomy/Burkholderia xenovorans_taxonomy_NA b/...onomy/Burkholderia xenovorans_taxonomy_NA → ...onomy/Burkholderia xenovorans_taxonomy_NA
diff --git a/..._taxonomy/Caenorhabditis elegans_taxonomy → ..._taxonomy/Caenorhabditis elegans_taxonomy b/..._taxonomy/Caenorhabditis elegans_taxonomy → ..._taxonomy/Caenorhabditis elegans_taxonomy
diff --git a/...rraneus subsp. tengcongensis MB4_taxonomy → ...rraneus subsp. tengcongensis MB4_taxonomy b/...rraneus subsp. tengcongensis MB4_taxonomy → ...rraneus subsp. tengcongensis MB4_taxonomy
diff --git a/...ubterraneus subsp. tengcongensis_taxonomy → ...ubterraneus subsp. tengcongensis_taxonomy b/...ubterraneus subsp. tengcongensis_taxonomy → ...ubterraneus subsp. tengcongensis_taxonomy
diff --git a/...icellulosiruptor saccharolyticus_taxonomy → ...icellulosiruptor saccharolyticus_taxonomy b/...icellulosiruptor saccharolyticus_taxonomy → ...icellulosiruptor saccharolyticus_taxonomy
diff --git a/...he/ncbi_taxonomy/Camelina sativa_taxonomy → ...he/ncbi_taxonomy/Camelina sativa_taxonomy b/...he/ncbi_taxonomy/Camelina sativa_taxonomy → ...he/ncbi_taxonomy/Camelina sativa_taxonomy
diff --git a/...cbi_taxonomy/Camelus dromedarius_taxonomy → ...cbi_taxonomy/Camelus dromedarius_taxonomy b/...cbi_taxonomy/Camelus dromedarius_taxonomy → ...cbi_taxonomy/Camelus dromedarius_taxonomy
diff --git a/...bi_taxonomy/Campylobacter jejuni_taxonomy → ...bi_taxonomy/Campylobacter jejuni_taxonomy b/...bi_taxonomy/Campylobacter jejuni_taxonomy → ...bi_taxonomy/Campylobacter jejuni_taxonomy
diff --git a/...bi_taxonomy/Canavalia ensiformis_taxonomy → ...bi_taxonomy/Canavalia ensiformis_taxonomy b/...bi_taxonomy/Canavalia ensiformis_taxonomy → ...bi_taxonomy/Canavalia ensiformis_taxonomy
diff --git a/...e/ncbi_taxonomy/Candida albicans_taxonomy → ...e/ncbi_taxonomy/Candida albicans_taxonomy b/...e/ncbi_taxonomy/Candida albicans_taxonomy → ...e/ncbi_taxonomy/Candida albicans_taxonomy
diff --git a/...cbi_taxonomy/Candida glabrata_taxonomy_NA → ...cbi_taxonomy/Candida glabrata_taxonomy_NA b/...cbi_taxonomy/Candida glabrata_taxonomy_NA → ...cbi_taxonomy/Candida glabrata_taxonomy_NA
diff --git a/...i_taxonomy/Candida intermedia_taxonomy_NA → ...i_taxonomy/Candida intermedia_taxonomy_NA b/...i_taxonomy/Candida intermedia_taxonomy_NA → ...i_taxonomy/Candida intermedia_taxonomy_NA
diff --git a/...bi_taxonomy/Candida mycoderma_taxonomy_NA → ...bi_taxonomy/Candida mycoderma_taxonomy_NA b/...bi_taxonomy/Candida mycoderma_taxonomy_NA → ...bi_taxonomy/Candida mycoderma_taxonomy_NA
diff --git a/.../ncbi_taxonomy/Candida tenuis_taxonomy_NA → .../ncbi_taxonomy/Candida tenuis_taxonomy_NA b/.../ncbi_taxonomy/Candida tenuis_taxonomy_NA → .../ncbi_taxonomy/Candida tenuis_taxonomy_NA
diff --git a/...ncbi_taxonomy/Candida tropicalis_taxonomy → ...ncbi_taxonomy/Candida tropicalis_taxonomy b/...ncbi_taxonomy/Candida tropicalis_taxonomy → ...ncbi_taxonomy/Candida tropicalis_taxonomy
diff --git a/...axonomy/Canid alphaherpesvirus 1_taxonomy → ...axonomy/Canid alphaherpesvirus 1_taxonomy b/...axonomy/Canid alphaherpesvirus 1_taxonomy → ...axonomy/Canid alphaherpesvirus 1_taxonomy
diff --git a/..._taxonomy/Canis lupus familiaris_taxonomy → ..._taxonomy/Canis lupus familiaris_taxonomy b/..._taxonomy/Canis lupus familiaris_taxonomy → ..._taxonomy/Canis lupus familiaris_taxonomy
diff --git a/...en/_cache/ncbi_taxonomy/Capitata_taxonomy → _cache/ncbi_taxonomy/Capitata_taxonomy b/...en/_cache/ncbi_taxonomy/Capitata_taxonomy → _cache/ncbi_taxonomy/Capitata_taxonomy
diff --git a/...che/ncbi_taxonomy/Capra capra_taxonomy_NA → _cache/ncbi_taxonomy/Capra capra_taxonomy_NA b/...che/ncbi_taxonomy/Capra capra_taxonomy_NA → _cache/ncbi_taxonomy/Capra capra_taxonomy_NA
diff --git a/...acmen/_cache/ncbi_taxonomy/Capra_taxonomy → _cache/ncbi_taxonomy/Capra_taxonomy b/...acmen/_cache/ncbi_taxonomy/Capra_taxonomy → _cache/ncbi_taxonomy/Capra_taxonomy
diff --git a/...cbi_taxonomy/Capsicum frutescens_taxonomy → ...cbi_taxonomy/Capsicum frutescens_taxonomy b/...cbi_taxonomy/Capsicum frutescens_taxonomy → ...cbi_taxonomy/Capsicum frutescens_taxonomy
diff --git a/.../ncbi_taxonomy/Carassius auratus_taxonomy → .../ncbi_taxonomy/Carassius auratus_taxonomy b/.../ncbi_taxonomy/Carassius auratus_taxonomy → .../ncbi_taxonomy/Carassius auratus_taxonomy
diff --git a/...arboxydothermus hydrogenoformans_taxonomy → ...arboxydothermus hydrogenoformans_taxonomy b/...arboxydothermus hydrogenoformans_taxonomy → ...arboxydothermus hydrogenoformans_taxonomy
diff --git a/..._taxonomy/Caulobacter vibrioides_taxonomy → ..._taxonomy/Caulobacter vibrioides_taxonomy b/..._taxonomy/Caulobacter vibrioides_taxonomy → ..._taxonomy/Caulobacter vibrioides_taxonomy
diff --git a/...he/ncbi_taxonomy/Cavia porcellus_taxonomy → ...he/ncbi_taxonomy/Cavia porcellus_taxonomy b/...he/ncbi_taxonomy/Cavia porcellus_taxonomy → ...he/ncbi_taxonomy/Cavia porcellus_taxonomy
diff --git a/...e/ncbi_taxonomy/Cellulomonas sp._taxonomy → ...e/ncbi_taxonomy/Cellulomonas sp._taxonomy b/...e/ncbi_taxonomy/Cellulomonas sp._taxonomy → ...e/ncbi_taxonomy/Cellulomonas sp._taxonomy
diff --git a/...ncbi_taxonomy/Ceratitis capitata_taxonomy → ...ncbi_taxonomy/Ceratitis capitata_taxonomy b/...ncbi_taxonomy/Ceratitis capitata_taxonomy → ...ncbi_taxonomy/Ceratitis capitata_taxonomy
diff --git a/...cbi_taxonomy/Chionodraco hamatus_taxonomy → ...cbi_taxonomy/Chionodraco hamatus_taxonomy b/...cbi_taxonomy/Chionodraco hamatus_taxonomy → ...cbi_taxonomy/Chionodraco hamatus_taxonomy
diff --git a/...bi_taxonomy/Chlamydia pneumoniae_taxonomy → ...bi_taxonomy/Chlamydia pneumoniae_taxonomy b/...bi_taxonomy/Chlamydia pneumoniae_taxonomy → ...bi_taxonomy/Chlamydia pneumoniae_taxonomy
diff --git a/...i_taxonomy/Chlamydia trachomatis_taxonomy → ...i_taxonomy/Chlamydia trachomatis_taxonomy b/...i_taxonomy/Chlamydia trachomatis_taxonomy → ...i_taxonomy/Chlamydia trachomatis_taxonomy
diff --git a/...xonomy/Chlamydomonas reinhardtii_taxonomy → ...xonomy/Chlamydomonas reinhardtii_taxonomy b/...xonomy/Chlamydomonas reinhardtii_taxonomy → ...xonomy/Chlamydomonas reinhardtii_taxonomy
diff --git a/...bi_taxonomy/Chlamydomonas sp._taxonomy_NA → ...bi_taxonomy/Chlamydomonas sp._taxonomy_NA b/...bi_taxonomy/Chlamydomonas sp._taxonomy_NA → ...bi_taxonomy/Chlamydomonas sp._taxonomy_NA
diff --git a/...nomy/Chlamydophila pneumoniae_taxonomy_NA → ...nomy/Chlamydophila pneumoniae_taxonomy_NA b/...nomy/Chlamydophila pneumoniae_taxonomy_NA → ...nomy/Chlamydophila pneumoniae_taxonomy_NA
diff --git a/...i_taxonomy/Chlorobaculum tepidum_taxonomy → ...i_taxonomy/Chlorobaculum tepidum_taxonomy b/...i_taxonomy/Chlorobaculum tepidum_taxonomy → ...i_taxonomy/Chlorobaculum tepidum_taxonomy
diff --git a/...axonomy/Chloroflexus aurantiacus_taxonomy → ...axonomy/Chloroflexus aurantiacus_taxonomy b/...axonomy/Chloroflexus aurantiacus_taxonomy → ...axonomy/Chloroflexus aurantiacus_taxonomy
diff --git a/...xonomy/Chromobacterium violaceum_taxonomy → ...xonomy/Chromobacterium violaceum_taxonomy b/...xonomy/Chromobacterium violaceum_taxonomy → ...xonomy/Chromobacterium violaceum_taxonomy
diff --git a/...bi_taxonomy/Citrobacter freundii_taxonomy → ...bi_taxonomy/Citrobacter freundii_taxonomy b/...bi_taxonomy/Citrobacter freundii_taxonomy → ...bi_taxonomy/Citrobacter freundii_taxonomy
diff --git a/...bi_taxonomy/Citrobacter sp. S-77_taxonomy → ...bi_taxonomy/Citrobacter sp. S-77_taxonomy b/...bi_taxonomy/Citrobacter sp. S-77_taxonomy → ...bi_taxonomy/Citrobacter sp. S-77_taxonomy
diff --git a/...he/ncbi_taxonomy/Citrobacter sp._taxonomy → ...he/ncbi_taxonomy/Citrobacter sp._taxonomy b/...he/ncbi_taxonomy/Citrobacter sp._taxonomy → ...he/ncbi_taxonomy/Citrobacter sp._taxonomy
diff --git a/...nomy/Classical swine fever virus_taxonomy → ...nomy/Classical swine fever virus_taxonomy b/...nomy/Classical swine fever virus_taxonomy → ...nomy/Classical swine fever virus_taxonomy
diff --git a/...cbi_taxonomy/Clonorchis sinensis_taxonomy → ...cbi_taxonomy/Clonorchis sinensis_taxonomy b/...cbi_taxonomy/Clonorchis sinensis_taxonomy → ...cbi_taxonomy/Clonorchis sinensis_taxonomy
diff --git a/...axonomy/Clostridioides difficile_taxonomy → ...axonomy/Clostridioides difficile_taxonomy b/...axonomy/Clostridioides difficile_taxonomy → ...axonomy/Clostridioides difficile_taxonomy
diff --git a/...onomy/Clostridium acetobutylicum_taxonomy → ...onomy/Clostridium acetobutylicum_taxonomy b/...onomy/Clostridium acetobutylicum_taxonomy → ...onomy/Clostridium acetobutylicum_taxonomy
diff --git a/...taxonomy/Clostridium perfringens_taxonomy → ...taxonomy/Clostridium perfringens_taxonomy b/...taxonomy/Clostridium perfringens_taxonomy → ...taxonomy/Clostridium perfringens_taxonomy
diff --git a/...he/ncbi_taxonomy/Clostridium sp._taxonomy → ...he/ncbi_taxonomy/Clostridium sp._taxonomy b/...he/ncbi_taxonomy/Clostridium sp._taxonomy → ...he/ncbi_taxonomy/Clostridium sp._taxonomy
diff --git a/...onomy/Clostridium sticklandii_taxonomy_NA → ...onomy/Clostridium sticklandii_taxonomy_NA b/...onomy/Clostridium sticklandii_taxonomy_NA → ...onomy/Clostridium sticklandii_taxonomy_NA
diff --git a/...nomy/Clostridium thermocellum_taxonomy_NA → ...nomy/Clostridium thermocellum_taxonomy_NA b/...nomy/Clostridium thermocellum_taxonomy_NA → ...nomy/Clostridium thermocellum_taxonomy_NA
diff --git a/...che/ncbi_taxonomy/Cobetia marina_taxonomy → _cache/ncbi_taxonomy/Cobetia marina_taxonomy b/...che/ncbi_taxonomy/Cobetia marina_taxonomy → _cache/ncbi_taxonomy/Cobetia marina_taxonomy
diff --git a/...ache/ncbi_taxonomy/Columba livia_taxonomy → _cache/ncbi_taxonomy/Columba livia_taxonomy b/...ache/ncbi_taxonomy/Columba livia_taxonomy → _cache/ncbi_taxonomy/Columba livia_taxonomy
diff --git a/..._cache/ncbi_taxonomy/Columba sp._taxonomy → _cache/ncbi_taxonomy/Columba sp._taxonomy b/..._cache/ncbi_taxonomy/Columba sp._taxonomy → _cache/ncbi_taxonomy/Columba sp._taxonomy
diff --git a/...he/ncbi_taxonomy/Colwellia maris_taxonomy → ...he/ncbi_taxonomy/Colwellia maris_taxonomy b/...he/ncbi_taxonomy/Colwellia maris_taxonomy → ...he/ncbi_taxonomy/Colwellia maris_taxonomy
diff --git a/...xonomy/Colwellia psychrerythraea_taxonomy → ...xonomy/Colwellia psychrerythraea_taxonomy b/...xonomy/Colwellia psychrerythraea_taxonomy → ...xonomy/Colwellia psychrerythraea_taxonomy
diff --git a/..._taxonomy/Comamonas testosteroni_taxonomy → ..._taxonomy/Comamonas testosteroni_taxonomy b/..._taxonomy/Comamonas testosteroni_taxonomy → ..._taxonomy/Comamonas testosteroni_taxonomy
diff --git a/...taxonomy/Conticribra weissflogii_taxonomy → ...taxonomy/Conticribra weissflogii_taxonomy b/...taxonomy/Conticribra weissflogii_taxonomy → ...taxonomy/Conticribra weissflogii_taxonomy
diff --git a/...omy/Corynebacterium ammoniagenes_taxonomy → ...omy/Corynebacterium ammoniagenes_taxonomy b/...omy/Corynebacterium ammoniagenes_taxonomy → ...omy/Corynebacterium ammoniagenes_taxonomy
diff --git a/...axonomy/Corynebacterium callunae_taxonomy → ...axonomy/Corynebacterium callunae_taxonomy b/...axonomy/Corynebacterium callunae_taxonomy → ...axonomy/Corynebacterium callunae_taxonomy
diff --git a/...axonomy/Corynebacterium crenatum_taxonomy → ...axonomy/Corynebacterium crenatum_taxonomy b/...axonomy/Corynebacterium crenatum_taxonomy → ...axonomy/Corynebacterium crenatum_taxonomy
diff --git a/...tamicum subsp. lactofermentum_taxonomy_NA → ...tamicum subsp. lactofermentum_taxonomy_NA b/...tamicum subsp. lactofermentum_taxonomy_NA → ...tamicum subsp. lactofermentum_taxonomy_NA
diff --git a/...onomy/Corynebacterium glutamicum_taxonomy → ...onomy/Corynebacterium glutamicum_taxonomy b/...onomy/Corynebacterium glutamicum_taxonomy → ...onomy/Corynebacterium glutamicum_taxonomy
diff --git a/...axonomy/Corynebacterium sp. U-96_taxonomy → ...axonomy/Corynebacterium sp. U-96_taxonomy b/...axonomy/Corynebacterium sp. U-96_taxonomy → ...axonomy/Corynebacterium sp. U-96_taxonomy
diff --git a/...cbi_taxonomy/Corynebacterium sp._taxonomy → ...cbi_taxonomy/Corynebacterium sp._taxonomy b/...cbi_taxonomy/Corynebacterium sp._taxonomy → ...cbi_taxonomy/Corynebacterium sp._taxonomy
diff --git a/...my/Coturnix coturnix japonica_taxonomy_NA → ...my/Coturnix coturnix japonica_taxonomy_NA b/...my/Coturnix coturnix japonica_taxonomy_NA → ...my/Coturnix coturnix japonica_taxonomy_NA
diff --git a/.../ncbi_taxonomy/Coturnix coturnix_taxonomy → .../ncbi_taxonomy/Coturnix coturnix_taxonomy b/.../ncbi_taxonomy/Coturnix coturnix_taxonomy → .../ncbi_taxonomy/Coturnix coturnix_taxonomy
diff --git a/.../ncbi_taxonomy/Coturnix japonica_taxonomy → .../ncbi_taxonomy/Coturnix japonica_taxonomy b/.../ncbi_taxonomy/Coturnix japonica_taxonomy → .../ncbi_taxonomy/Coturnix japonica_taxonomy
diff --git a/.../_cache/ncbi_taxonomy/Cricetinae_taxonomy → _cache/ncbi_taxonomy/Cricetinae_taxonomy b/.../_cache/ncbi_taxonomy/Cricetinae_taxonomy → _cache/ncbi_taxonomy/Cricetinae_taxonomy
diff --git a/...ncbi_taxonomy/Cricetulus griseus_taxonomy → ...ncbi_taxonomy/Cricetulus griseus_taxonomy b/...ncbi_taxonomy/Cricetulus griseus_taxonomy → ...ncbi_taxonomy/Cricetulus griseus_taxonomy
diff --git a/...che/ncbi_taxonomy/Cricetulus sp._taxonomy → _cache/ncbi_taxonomy/Cricetulus sp._taxonomy b/...che/ncbi_taxonomy/Cricetulus sp._taxonomy → _cache/ncbi_taxonomy/Cricetulus sp._taxonomy
diff --git a/...i_taxonomy/Crithidia fasciculata_taxonomy → ...i_taxonomy/Crithidia fasciculata_taxonomy b/...i_taxonomy/Crithidia fasciculata_taxonomy → ...i_taxonomy/Crithidia fasciculata_taxonomy
diff --git a/...cbi_taxonomy/Crotalus adamanteus_taxonomy → ...cbi_taxonomy/Crotalus adamanteus_taxonomy b/...cbi_taxonomy/Crotalus adamanteus_taxonomy → ...cbi_taxonomy/Crotalus adamanteus_taxonomy
diff --git a/..._taxonomy/Cryptococcus flavus_taxonomy_NA → ..._taxonomy/Cryptococcus flavus_taxonomy_NA b/..._taxonomy/Cryptococcus flavus_taxonomy_NA → ..._taxonomy/Cryptococcus flavus_taxonomy_NA
diff --git a/...taxonomy/Cryptococcus neoformans_taxonomy → ...taxonomy/Cryptococcus neoformans_taxonomy b/...taxonomy/Cryptococcus neoformans_taxonomy → ...taxonomy/Cryptococcus neoformans_taxonomy
diff --git a/..._taxonomy/Cryptosporidium parvum_taxonomy → ..._taxonomy/Cryptosporidium parvum_taxonomy b/..._taxonomy/Cryptosporidium parvum_taxonomy → ..._taxonomy/Cryptosporidium parvum_taxonomy
diff --git a/...he/ncbi_taxonomy/Cucumis sativus_taxonomy → ...he/ncbi_taxonomy/Cucumis sativus_taxonomy b/...he/ncbi_taxonomy/Cucumis sativus_taxonomy → ...he/ncbi_taxonomy/Cucumis sativus_taxonomy
diff --git a/...cbi_taxonomy/Cupriavidus necator_taxonomy → ...cbi_taxonomy/Cupriavidus necator_taxonomy b/...cbi_taxonomy/Cupriavidus necator_taxonomy → ...cbi_taxonomy/Cupriavidus necator_taxonomy
diff --git a/...cbi_taxonomy/Cyanidium caldarium_taxonomy → ...cbi_taxonomy/Cyanidium caldarium_taxonomy b/...cbi_taxonomy/Cyanidium caldarium_taxonomy → ...cbi_taxonomy/Cyanidium caldarium_taxonomy
diff --git a/...cbi_taxonomy/Cyanophora paradoxa_taxonomy → ...cbi_taxonomy/Cyanophora paradoxa_taxonomy b/...cbi_taxonomy/Cyanophora paradoxa_taxonomy → ...cbi_taxonomy/Cyanophora paradoxa_taxonomy
diff --git a/...i_taxonomy/Cyberlindnera jadinii_taxonomy → ...i_taxonomy/Cyberlindnera jadinii_taxonomy b/...i_taxonomy/Cyberlindnera jadinii_taxonomy → ...i_taxonomy/Cyberlindnera jadinii_taxonomy
diff --git a/...he/ncbi_taxonomy/Cyprinus carpio_taxonomy → ...he/ncbi_taxonomy/Cyprinus carpio_taxonomy b/...he/ncbi_taxonomy/Cyprinus carpio_taxonomy → ...he/ncbi_taxonomy/Cyprinus carpio_taxonomy
diff --git a/..._taxonomy/Cytophaga hutchinsonii_taxonomy → ..._taxonomy/Cytophaga hutchinsonii_taxonomy b/..._taxonomy/Cytophaga hutchinsonii_taxonomy → ..._taxonomy/Cytophaga hutchinsonii_taxonomy
diff --git a/..._cache/ncbi_taxonomy/Danio rerio_taxonomy → _cache/ncbi_taxonomy/Danio rerio_taxonomy b/..._cache/ncbi_taxonomy/Danio rerio_taxonomy → _cache/ncbi_taxonomy/Danio rerio_taxonomy
diff --git a/...ncbi_taxonomy/Dasyatis pastinaca_taxonomy → ...ncbi_taxonomy/Dasyatis pastinaca_taxonomy b/...ncbi_taxonomy/Dasyatis pastinaca_taxonomy → ...ncbi_taxonomy/Dasyatis pastinaca_taxonomy
diff --git a/...ache/ncbi_taxonomy/Daucus carota_taxonomy → _cache/ncbi_taxonomy/Daucus carota_taxonomy b/...ache/ncbi_taxonomy/Daucus carota_taxonomy → _cache/ncbi_taxonomy/Daucus carota_taxonomy
diff --git a/...i_taxonomy/Debaryomyces hansenii_taxonomy → ...i_taxonomy/Debaryomyces hansenii_taxonomy b/...i_taxonomy/Debaryomyces hansenii_taxonomy → ...i_taxonomy/Debaryomyces hansenii_taxonomy
diff --git a/..._taxonomy/Deinagkistrodon acutus_taxonomy → ..._taxonomy/Deinagkistrodon acutus_taxonomy b/..._taxonomy/Deinagkistrodon acutus_taxonomy → ..._taxonomy/Deinagkistrodon acutus_taxonomy
diff --git a/...taxonomy/Deinococcus radiodurans_taxonomy → ...taxonomy/Deinococcus radiodurans_taxonomy b/...taxonomy/Deinococcus radiodurans_taxonomy → ...taxonomy/Deinococcus radiodurans_taxonomy
diff --git a/...cbi_taxonomy/Delftia acidovorans_taxonomy → ...cbi_taxonomy/Delftia acidovorans_taxonomy b/...cbi_taxonomy/Delftia acidovorans_taxonomy → ...cbi_taxonomy/Delftia acidovorans_taxonomy
diff --git a/..._cache/ncbi_taxonomy/Delftia sp._taxonomy → _cache/ncbi_taxonomy/Delftia sp._taxonomy b/..._cache/ncbi_taxonomy/Delftia sp._taxonomy → _cache/ncbi_taxonomy/Delftia sp._taxonomy
diff --git a/...xonomy/Desulfotalea psychrophila_taxonomy → ...xonomy/Desulfotalea psychrophila_taxonomy b/...xonomy/Desulfotalea psychrophila_taxonomy → ...xonomy/Desulfotalea psychrophila_taxonomy
diff --git a/...cbi_taxonomy/Desulfovibrio gigas_taxonomy → ...cbi_taxonomy/Desulfovibrio gigas_taxonomy b/...cbi_taxonomy/Desulfovibrio gigas_taxonomy → ...cbi_taxonomy/Desulfovibrio gigas_taxonomy
diff --git a/...omy/Desulfurococcus amylolyticus_taxonomy → ...omy/Desulfurococcus amylolyticus_taxonomy b/...omy/Desulfurococcus amylolyticus_taxonomy → ...omy/Desulfurococcus amylolyticus_taxonomy
diff --git a/...bi_taxonomy/Dickeya chrysanthemi_taxonomy → ...bi_taxonomy/Dickeya chrysanthemi_taxonomy b/...bi_taxonomy/Dickeya chrysanthemi_taxonomy → ...bi_taxonomy/Dickeya chrysanthemi_taxonomy
diff --git a/...i_taxonomy/Dictyoglomus turgidum_taxonomy → ...i_taxonomy/Dictyoglomus turgidum_taxonomy b/...i_taxonomy/Dictyoglomus turgidum_taxonomy → ...i_taxonomy/Dictyoglomus turgidum_taxonomy
diff --git a/...axonomy/Dictyostelium discoideum_taxonomy → ...axonomy/Dictyostelium discoideum_taxonomy b/...axonomy/Dictyostelium discoideum_taxonomy → ...axonomy/Dictyostelium discoideum_taxonomy
diff --git a/.../ncbi_taxonomy/Dictyostelium sp._taxonomy → .../ncbi_taxonomy/Dictyostelium sp._taxonomy b/.../ncbi_taxonomy/Dictyostelium sp._taxonomy → .../ncbi_taxonomy/Dictyostelium sp._taxonomy
diff --git a/...cbi_taxonomy/Dirofilaria immitis_taxonomy → ...cbi_taxonomy/Dirofilaria immitis_taxonomy b/...cbi_taxonomy/Dirofilaria immitis_taxonomy → ...cbi_taxonomy/Dirofilaria immitis_taxonomy
diff --git a/...onomy/Drosophila lebanonensis_taxonomy_NA → ...onomy/Drosophila lebanonensis_taxonomy_NA b/...onomy/Drosophila lebanonensis_taxonomy_NA → ...onomy/Drosophila lebanonensis_taxonomy_NA
diff --git a/...taxonomy/Drosophila melanogaster_taxonomy → ...taxonomy/Drosophila melanogaster_taxonomy b/...taxonomy/Drosophila melanogaster_taxonomy → ...taxonomy/Drosophila melanogaster_taxonomy
diff --git a/.../ncbi_taxonomy/Dunaliella salina_taxonomy → .../ncbi_taxonomy/Dunaliella salina_taxonomy b/.../ncbi_taxonomy/Dunaliella salina_taxonomy → .../ncbi_taxonomy/Dunaliella salina_taxonomy
diff --git a/...bi_taxonomy/Dysdercus peruvianus_taxonomy → ...bi_taxonomy/Dysdercus peruvianus_taxonomy b/...bi_taxonomy/Dysdercus peruvianus_taxonomy → ...bi_taxonomy/Dysdercus peruvianus_taxonomy
diff --git a/...i_taxonomy/Edwardsiella ictaluri_taxonomy → ...i_taxonomy/Edwardsiella ictaluri_taxonomy b/...i_taxonomy/Edwardsiella ictaluri_taxonomy → ...i_taxonomy/Edwardsiella ictaluri_taxonomy
diff --git a/...he/ncbi_taxonomy/Eimeria tenella_taxonomy → ...he/ncbi_taxonomy/Eimeria tenella_taxonomy b/...he/ncbi_taxonomy/Eimeria tenella_taxonomy → ...he/ncbi_taxonomy/Eimeria tenella_taxonomy
diff --git a/...che/ncbi_taxonomy/Eisenia fetida_taxonomy → _cache/ncbi_taxonomy/Eisenia fetida_taxonomy b/...che/ncbi_taxonomy/Eisenia fetida_taxonomy → _cache/ncbi_taxonomy/Eisenia fetida_taxonomy
diff --git a/...i_taxonomy/Entamoeba histolytica_taxonomy → ...i_taxonomy/Entamoeba histolytica_taxonomy b/...i_taxonomy/Entamoeba histolytica_taxonomy → ...i_taxonomy/Entamoeba histolytica_taxonomy
diff --git a/...bi_taxonomy/Enterobacter cloacae_taxonomy → ...bi_taxonomy/Enterobacter cloacae_taxonomy b/...bi_taxonomy/Enterobacter cloacae_taxonomy → ...bi_taxonomy/Enterobacter cloacae_taxonomy
diff --git a/...e/ncbi_taxonomy/Enterobacter sp._taxonomy → ...e/ncbi_taxonomy/Enterobacter sp._taxonomy b/...e/ncbi_taxonomy/Enterobacter sp._taxonomy → ...e/ncbi_taxonomy/Enterobacter sp._taxonomy
diff --git a/...taxonomy/Enterobacteria phage T2_taxonomy → ...taxonomy/Enterobacteria phage T2_taxonomy b/...taxonomy/Enterobacteria phage T2_taxonomy → ...taxonomy/Enterobacteria phage T2_taxonomy
diff --git a/...i_taxonomy/Enterococcus faecalis_taxonomy → ...i_taxonomy/Enterococcus faecalis_taxonomy b/...i_taxonomy/Enterococcus faecalis_taxonomy → ...i_taxonomy/Enterococcus faecalis_taxonomy
diff --git a/...bi_taxonomy/Enterococcus faecium_taxonomy → ...bi_taxonomy/Enterococcus faecium_taxonomy b/...bi_taxonomy/Enterococcus faecium_taxonomy → ...bi_taxonomy/Enterococcus faecium_taxonomy
diff --git a/...taxonomy/Enterococcus gallinarum_taxonomy → ...taxonomy/Enterococcus gallinarum_taxonomy b/...taxonomy/Enterococcus gallinarum_taxonomy → ...taxonomy/Enterococcus gallinarum_taxonomy
diff --git a/...e/ncbi_taxonomy/Enterococcus sp._taxonomy → ...e/ncbi_taxonomy/Enterococcus sp._taxonomy b/...e/ncbi_taxonomy/Enterococcus sp._taxonomy → ...e/ncbi_taxonomy/Enterococcus sp._taxonomy
diff --git a/...i_taxonomy/Epstein-Barr virus_taxonomy_NA → ...i_taxonomy/Epstein-Barr virus_taxonomy_NA b/...i_taxonomy/Epstein-Barr virus_taxonomy_NA → ...i_taxonomy/Epstein-Barr virus_taxonomy_NA
diff --git a/...y/Equine infectious anemia virus_taxonomy → ...y/Equine infectious anemia virus_taxonomy b/...y/Equine infectious anemia virus_taxonomy → ...y/Equine infectious anemia virus_taxonomy
diff --git a/...che/ncbi_taxonomy/Equus caballus_taxonomy → _cache/ncbi_taxonomy/Equus caballus_taxonomy b/...che/ncbi_taxonomy/Equus caballus_taxonomy → _cache/ncbi_taxonomy/Equus caballus_taxonomy
diff --git a/...i_taxonomy/Eremothecium gossypii_taxonomy → ...i_taxonomy/Eremothecium gossypii_taxonomy b/...i_taxonomy/Eremothecium gossypii_taxonomy → ...i_taxonomy/Eremothecium gossypii_taxonomy
diff --git a/...taxonomy/Erwinia chrysanthemi_taxonomy_NA → ...taxonomy/Erwinia chrysanthemi_taxonomy_NA b/...taxonomy/Erwinia chrysanthemi_taxonomy_NA → ...taxonomy/Erwinia chrysanthemi_taxonomy_NA
diff --git a/...ncbi_taxonomy/Erwinia rhapontici_taxonomy → ...ncbi_taxonomy/Erwinia rhapontici_taxonomy b/...ncbi_taxonomy/Erwinia rhapontici_taxonomy → ...ncbi_taxonomy/Erwinia rhapontici_taxonomy
diff --git a/...omy/Erysipelothrix rhusiopathiae_taxonomy → ...omy/Erysipelothrix rhusiopathiae_taxonomy b/...omy/Erysipelothrix rhusiopathiae_taxonomy → ...omy/Erysipelothrix rhusiopathiae_taxonomy
diff --git a/.../ncbi_taxonomy/Erythroxylum coca_taxonomy → .../ncbi_taxonomy/Erythroxylum coca_taxonomy b/.../ncbi_taxonomy/Erythroxylum coca_taxonomy → .../ncbi_taxonomy/Erythroxylum coca_taxonomy
diff --git a/...i_taxonomy/Escherichia coli K-12_taxonomy → ...i_taxonomy/Escherichia coli K-12_taxonomy b/...i_taxonomy/Escherichia coli K-12_taxonomy → ...i_taxonomy/Escherichia coli K-12_taxonomy
diff --git a/...scherichia coli P31658 P31658_taxonomy_NA → ...scherichia coli P31658 P31658_taxonomy_NA b/...scherichia coli P31658 P31658_taxonomy_NA → ...scherichia coli P31658 P31658_taxonomy_NA
diff --git a/...onomy/Escherichia coli P76440_taxonomy_NA → ...onomy/Escherichia coli P76440_taxonomy_NA b/...onomy/Escherichia coli P76440_taxonomy_NA → ...onomy/Escherichia coli P76440_taxonomy_NA
diff --git a/...e/ncbi_taxonomy/Escherichia coli_taxonomy → ...e/ncbi_taxonomy/Escherichia coli_taxonomy b/...e/ncbi_taxonomy/Escherichia coli_taxonomy → ...e/ncbi_taxonomy/Escherichia coli_taxonomy
diff --git a/...bi_taxonomy/Escherichia virus T4_taxonomy → ...bi_taxonomy/Escherichia virus T4_taxonomy b/...bi_taxonomy/Escherichia virus T4_taxonomy → ...bi_taxonomy/Escherichia virus T4_taxonomy
diff --git a/...e/ncbi_taxonomy/Euglena gracilis_taxonomy → ...e/ncbi_taxonomy/Euglena gracilis_taxonomy b/...e/ncbi_taxonomy/Euglena gracilis_taxonomy → ...e/ncbi_taxonomy/Euglena gracilis_taxonomy
diff --git a/...cbi_taxonomy/Euphorbia characias_taxonomy → ...cbi_taxonomy/Euphorbia characias_taxonomy b/...cbi_taxonomy/Euphorbia characias_taxonomy → ...cbi_taxonomy/Euphorbia characias_taxonomy
diff --git a/...cbi_taxonomy/Exiguobacterium sp._taxonomy → ...cbi_taxonomy/Exiguobacterium sp._taxonomy b/...cbi_taxonomy/Exiguobacterium sp._taxonomy → ...cbi_taxonomy/Exiguobacterium sp._taxonomy
diff --git a/...axonomy/Felid alphaherpesvirus 1_taxonomy → ...axonomy/Felid alphaherpesvirus 1_taxonomy b/...axonomy/Felid alphaherpesvirus 1_taxonomy → ...axonomy/Felid alphaherpesvirus 1_taxonomy
diff --git a/..._cache/ncbi_taxonomy/Felis catus_taxonomy → _cache/ncbi_taxonomy/Felis catus_taxonomy b/..._cache/ncbi_taxonomy/Felis catus_taxonomy → _cache/ncbi_taxonomy/Felis catus_taxonomy
diff --git a/...taxonomy/Ferroplasma acidiphilum_taxonomy → ...taxonomy/Ferroplasma acidiphilum_taxonomy b/...taxonomy/Ferroplasma acidiphilum_taxonomy → ...taxonomy/Ferroplasma acidiphilum_taxonomy
diff --git a/...inogenes subsp. succinogenes S85_taxonomy → ...inogenes subsp. succinogenes S85_taxonomy b/...inogenes subsp. succinogenes S85_taxonomy → ...inogenes subsp. succinogenes S85_taxonomy
diff --git a/.../ncbi_taxonomy/Flaveria bidentis_taxonomy → .../ncbi_taxonomy/Flaveria bidentis_taxonomy b/.../ncbi_taxonomy/Flaveria bidentis_taxonomy → .../ncbi_taxonomy/Flaveria bidentis_taxonomy