LICENSE
README.md
setup.py
VirID/__init__.py
VirID/__main__.py
VirID/assembly_and_basic_annotation.py
VirID/cli.py
VirID/main.py
VirID/phylogenetic_analysis.py
VirID.egg-info/PKG-INFO
VirID.egg-info/SOURCES.txt
VirID.egg-info/dependency_links.txt
VirID.egg-info/entry_points.txt
VirID.egg-info/requires.txt
VirID.egg-info/top_level.txt
VirID/biolib/__init__.py
VirID/biolib/common.py
VirID/biolib/custom_help_formatter.py
VirID/biolib/exceptions.py
VirID/biolib/logger.py
VirID/biolib/../__init__.py
VirID/biolib/../__main__.py
VirID/biolib/../assembly_and_basic_annotation.py
VirID/biolib/../cli.py
VirID/biolib/../main.py
VirID/biolib/../phylogenetic_analysis.py
VirID/biolib/../config/__init__.py
VirID/biolib/../config/config.py
VirID/biolib/../data/ICTV_TAXON.csv
VirID/biolib/../data/Pathogenicity_VIRUS_CSV.csv
VirID/biolib/../data/RdRP_ICTV_NR.csv
VirID/biolib/../data/__init__.py
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.fas
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.pdf
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.csv
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.fas
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.pdf
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto.csv
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto.fas
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto.pdf
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi.csv
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi.fas
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi.pdf
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo.csv
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo.fas
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo.pdf
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.fas
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.pdf
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.fas
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.pdf
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.pdf
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.pdf
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.pdf
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido.csv
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido.fas
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido.pdf
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.fas
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.pdf
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.fas
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus.fas
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus.pdf
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Qinvirus/Qinvirus_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo.csv
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo.fas
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo.pdf
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.csv
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.fas
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Tombus-Noda/Tombus-noda.pdf
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.csv
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.fas
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.pdf
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus.csv
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus.fas
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus.pdf
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus.csv
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus.fas
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus.pdf
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus.csv
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus.fas
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus.pdf
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.csv
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.fas
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.pdf
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi.csv
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi.fas
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi.pdf
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.phy
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative.csv
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative.fas
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative.pdf
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative.phy_phyml_tree.nwk
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_info.txt
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_result.nwk
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.fas
VirID/biolib/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.phy
VirID/biolib/../data/diamond_database/RdRP_230330_rmdup.fas
VirID/biolib/../data/diamond_database/RdRp_expanded_20230330.csv
VirID/biolib/../external/__init__.py
VirID/biolib/../external/align_trim.py
VirID/biolib/../external/blast.py
VirID/biolib/../external/fasta_process.py
VirID/biolib/../external/reads_tool.py
VirID/biolib/../external/tree_build.py
VirID/biolib/../phytree/__init__.py
VirID/biolib/../phytree/classify.py
VirID/biolib/../phytree/infectivity_distribution.r
VirID/biolib/../phytree/label_tree.r
VirID/biolib/../phytree/translate.py
VirID/biolib/../phytree/tree_taxon.py
VirID/biolib/../rvm/__init__.py
VirID/biolib/../rvm/anicalc.py
VirID/biolib/../rvm/aniclust.py
VirID/biolib/../rvm/calculate_RPM.py
VirID/biolib/../rvm/histogram.py
VirID/biolib/../rvm/main_taxon.py
VirID/biolib/../rvm/rmdup.py
VirID/biolib/../rvm/sankey.r
VirID/biolib/../rvm/summary.py
VirID/biolib/../rvm/trim_contamination.py
VirID/config/__init__.py
VirID/config/config.py
VirID/config/../__init__.py
VirID/config/../__main__.py
VirID/config/../assembly_and_basic_annotation.py
VirID/config/../cli.py
VirID/config/../main.py
VirID/config/../phylogenetic_analysis.py
VirID/config/../biolib/__init__.py
VirID/config/../biolib/common.py
VirID/config/../biolib/custom_help_formatter.py
VirID/config/../biolib/exceptions.py
VirID/config/../biolib/logger.py
VirID/config/../data/ICTV_TAXON.csv
VirID/config/../data/Pathogenicity_VIRUS_CSV.csv
VirID/config/../data/RdRP_ICTV_NR.csv
VirID/config/../data/__init__.py
VirID/config/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
VirID/config/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.fas
VirID/config/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.pdf
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VirID/config/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_info.txt
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VirID/config/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.csv
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VirID/config/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Cysto/Cysto.csv
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VirID/config/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Flavi/Flavi.csv
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VirID/config/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Hypo/Hypo.csv
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VirID/config/../data/RdRP_tree_230328/Hypo/Hypo.pdf
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VirID/config/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
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VirID/config/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
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VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
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VirID/config/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
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VirID/config/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
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VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
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VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Nido/Nido.csv
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VirID/config/../data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/config/../data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/config/../data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/config/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
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VirID/config/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/config/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
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VirID/config/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/config/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/config/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
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VirID/config/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/config/../data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
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VirID/config/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
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VirID/config/../data/diamond_database/RdRP_230330_rmdup.fas
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VirID/config/../external/__init__.py
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VirID/config/../external/fasta_process.py
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VirID/config/../phytree/tree_taxon.py
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VirID/config/../rvm/anicalc.py
VirID/config/../rvm/aniclust.py
VirID/config/../rvm/calculate_RPM.py
VirID/config/../rvm/histogram.py
VirID/config/../rvm/main_taxon.py
VirID/config/../rvm/rmdup.py
VirID/config/../rvm/sankey.r
VirID/config/../rvm/summary.py
VirID/config/../rvm/trim_contamination.py
VirID/data/ICTV_TAXON.csv
VirID/data/Pathogenicity_VIRUS_CSV.csv
VirID/data/RdRP_ICTV_NR.csv
VirID/data/__init__.py
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VirID/data/../assembly_and_basic_annotation.py
VirID/data/../cli.py
VirID/data/../main.py
VirID/data/../phylogenetic_analysis.py
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VirID/data/../biolib/common.py
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VirID/data/../biolib/exceptions.py
VirID/data/../biolib/logger.py
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VirID/data/../config/config.py
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VirID/data/../external/align_trim.py
VirID/data/../external/blast.py
VirID/data/../external/fasta_process.py
VirID/data/../external/reads_tool.py
VirID/data/../external/tree_build.py
VirID/data/../phytree/__init__.py
VirID/data/../phytree/classify.py
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VirID/data/../phytree/label_tree.r
VirID/data/../phytree/translate.py
VirID/data/../phytree/tree_taxon.py
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VirID/data/../rvm/anicalc.py
VirID/data/../rvm/aniclust.py
VirID/data/../rvm/calculate_RPM.py
VirID/data/../rvm/histogram.py
VirID/data/../rvm/main_taxon.py
VirID/data/../rvm/rmdup.py
VirID/data/../rvm/sankey.r
VirID/data/../rvm/summary.py
VirID/data/../rvm/trim_contamination.py
VirID/data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
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VirID/data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
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VirID/data/RdRP_tree_230328/Cysto/Cysto.fas
VirID/data/RdRP_tree_230328/Cysto/Cysto.pdf
VirID/data/RdRP_tree_230328/Cysto/Cysto.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Flavi/Flavi.csv
VirID/data/RdRP_tree_230328/Flavi/Flavi.fas
VirID/data/RdRP_tree_230328/Flavi/Flavi.pdf
VirID/data/RdRP_tree_230328/Flavi/Flavi.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Hypo/Hypo.csv
VirID/data/RdRP_tree_230328/Hypo/Hypo.fas
VirID/data/RdRP_tree_230328/Hypo/Hypo.pdf
VirID/data/RdRP_tree_230328/Hypo/Hypo.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.fas
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.pdf
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi.fas
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi.pdf
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.fas
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.pdf
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.fas
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.pdf
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.pdf
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Nido/Nido.csv
VirID/data/RdRP_tree_230328/Nido/Nido.fas
VirID/data/RdRP_tree_230328/Nido/Nido.pdf
VirID/data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.fas
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.pdf
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_info.txt
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.fas
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus.fas
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus.pdf
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Qinvirus/Qinvirus_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Reo/Reo.csv
VirID/data/RdRP_tree_230328/Reo/Reo.fas
VirID/data/RdRP_tree_230328/Reo/Reo.pdf
VirID/data/RdRP_tree_230328/Reo/Reo.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Reo/Reo_RAxML_info.txt
VirID/data/RdRP_tree_230328/Reo/Reo_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.csv
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.fas
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_info.txt
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Tombus-Noda/Tombus-noda.pdf
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.csv
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.fas
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.pdf
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_info.txt
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Weivirus/Weivirus.csv
VirID/data/RdRP_tree_230328/Weivirus/Weivirus.fas
VirID/data/RdRP_tree_230328/Weivirus/Weivirus.pdf
VirID/data/RdRP_tree_230328/Weivirus/Weivirus.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_info.txt
VirID/data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus.csv
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus.fas
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus.pdf
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_info.txt
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus.csv
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus.fas
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus.pdf
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_info.txt
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus.csv
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus.fas
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus.pdf
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_info.txt
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_result.nwk
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/na-daxi/na-daxi.csv
VirID/data/RdRP_tree_230328/na-daxi/na-daxi.fas
VirID/data/RdRP_tree_230328/na-daxi/na-daxi.pdf
VirID/data/RdRP_tree_230328/na-daxi/na-daxi.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_info.txt
VirID/data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_result.nwk
VirID/data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.phy
VirID/data/RdRP_tree_230328/other-negative/other-negative.csv
VirID/data/RdRP_tree_230328/other-negative/other-negative.fas
VirID/data/RdRP_tree_230328/other-negative/other-negative.pdf
VirID/data/RdRP_tree_230328/other-negative/other-negative.phy_phyml_tree.nwk
VirID/data/RdRP_tree_230328/other-negative/other-negative_RAxML_info.txt
VirID/data/RdRP_tree_230328/other-negative/other-negative_RAxML_result.nwk
VirID/data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.fas
VirID/data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.phy
VirID/data/diamond_database/RdRP_230330_rmdup.fas
VirID/data/diamond_database/RdRp_expanded_20230330.csv
VirID/external/__init__.py
VirID/external/align_trim.py
VirID/external/blast.py
VirID/external/fasta_process.py
VirID/external/reads_tool.py
VirID/external/tree_build.py
VirID/external/../__init__.py
VirID/external/../__main__.py
VirID/external/../assembly_and_basic_annotation.py
VirID/external/../cli.py
VirID/external/../main.py
VirID/external/../phylogenetic_analysis.py
VirID/external/../biolib/__init__.py
VirID/external/../biolib/common.py
VirID/external/../biolib/custom_help_formatter.py
VirID/external/../biolib/exceptions.py
VirID/external/../biolib/logger.py
VirID/external/../config/__init__.py
VirID/external/../config/config.py
VirID/external/../data/ICTV_TAXON.csv
VirID/external/../data/Pathogenicity_VIRUS_CSV.csv
VirID/external/../data/RdRP_ICTV_NR.csv
VirID/external/../data/__init__.py
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.fas
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.pdf
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.csv
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.fas
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.pdf
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto.csv
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto.fas
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto.pdf
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi.csv
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi.fas
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi.pdf
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo.csv
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo.fas
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo.pdf
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.fas
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.pdf
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.fas
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.pdf
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.fas
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.pdf
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.fas
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.pdf
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.pdf
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Nido/Nido.csv
VirID/external/../data/RdRP_tree_230328/Nido/Nido.fas
VirID/external/../data/RdRP_tree_230328/Nido/Nido.pdf
VirID/external/../data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.fas
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.pdf
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.fas
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus.fas
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus.pdf
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Qinvirus/Qinvirus_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Reo/Reo.csv
VirID/external/../data/RdRP_tree_230328/Reo/Reo.fas
VirID/external/../data/RdRP_tree_230328/Reo/Reo.pdf
VirID/external/../data/RdRP_tree_230328/Reo/Reo.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Reo/Reo_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Reo/Reo_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.csv
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.fas
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Tombus-Noda/Tombus-noda.pdf
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.csv
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.fas
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.pdf
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus.csv
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus.fas
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus.pdf
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus.csv
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus.fas
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus.pdf
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus.csv
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus.fas
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus.pdf
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.csv
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.fas
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.pdf
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi.csv
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi.fas
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi.pdf
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.phy
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative.csv
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative.fas
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative.pdf
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative.phy_phyml_tree.nwk
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_info.txt
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_result.nwk
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.fas
VirID/external/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.phy
VirID/external/../data/diamond_database/RdRP_230330_rmdup.fas
VirID/external/../data/diamond_database/RdRp_expanded_20230330.csv
VirID/external/../phytree/__init__.py
VirID/external/../phytree/classify.py
VirID/external/../phytree/infectivity_distribution.r
VirID/external/../phytree/label_tree.r
VirID/external/../phytree/translate.py
VirID/external/../phytree/tree_taxon.py
VirID/external/../rvm/__init__.py
VirID/external/../rvm/anicalc.py
VirID/external/../rvm/aniclust.py
VirID/external/../rvm/calculate_RPM.py
VirID/external/../rvm/histogram.py
VirID/external/../rvm/main_taxon.py
VirID/external/../rvm/rmdup.py
VirID/external/../rvm/sankey.r
VirID/external/../rvm/summary.py
VirID/external/../rvm/trim_contamination.py
VirID/phytree/__init__.py
VirID/phytree/classify.py
VirID/phytree/infectivity_distribution.r
VirID/phytree/label_tree.r
VirID/phytree/translate.py
VirID/phytree/tree_taxon.py
VirID/phytree/../__init__.py
VirID/phytree/../__main__.py
VirID/phytree/../assembly_and_basic_annotation.py
VirID/phytree/../cli.py
VirID/phytree/../main.py
VirID/phytree/../phylogenetic_analysis.py
VirID/phytree/../biolib/__init__.py
VirID/phytree/../biolib/common.py
VirID/phytree/../biolib/custom_help_formatter.py
VirID/phytree/../biolib/exceptions.py
VirID/phytree/../biolib/logger.py
VirID/phytree/../config/__init__.py
VirID/phytree/../config/config.py
VirID/phytree/../data/ICTV_TAXON.csv
VirID/phytree/../data/Pathogenicity_VIRUS_CSV.csv
VirID/phytree/../data/RdRP_ICTV_NR.csv
VirID/phytree/../data/__init__.py
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.fas
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.pdf
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.csv
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.fas
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.pdf
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto.csv
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto.fas
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto.pdf
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi.csv
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi.fas
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi.pdf
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo.csv
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo.fas
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo.pdf
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.fas
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.pdf
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.fas
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.pdf
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.pdf
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.pdf
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.pdf
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido.csv
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VirID/phytree/../data/RdRP_tree_230328/Nido/Nido.pdf
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.fas
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.pdf
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.fas
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus.fas
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus.pdf
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Qinvirus/Qinvirus_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo.csv
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo.fas
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo.pdf
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.csv
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.fas
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Tombus-Noda/Tombus-noda.pdf
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.csv
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.fas
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.pdf
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus.csv
VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus.fas
VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus.pdf
VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_info.txt
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VirID/phytree/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.fas
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VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus.csv
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus.fas
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus.pdf
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.fas
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VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus.csv
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus.fas
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus.pdf
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.csv
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.fas
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.pdf
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi.csv
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi.fas
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi.pdf
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.phy
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative.csv
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative.fas
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative.pdf
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative.phy_phyml_tree.nwk
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_info.txt
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_result.nwk
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.fas
VirID/phytree/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.phy
VirID/phytree/../data/diamond_database/RdRP_230330_rmdup.fas
VirID/phytree/../data/diamond_database/RdRp_expanded_20230330.csv
VirID/phytree/../external/__init__.py
VirID/phytree/../external/align_trim.py
VirID/phytree/../external/blast.py
VirID/phytree/../external/fasta_process.py
VirID/phytree/../external/reads_tool.py
VirID/phytree/../external/tree_build.py
VirID/phytree/../rvm/__init__.py
VirID/phytree/../rvm/anicalc.py
VirID/phytree/../rvm/aniclust.py
VirID/phytree/../rvm/calculate_RPM.py
VirID/phytree/../rvm/histogram.py
VirID/phytree/../rvm/main_taxon.py
VirID/phytree/../rvm/rmdup.py
VirID/phytree/../rvm/sankey.r
VirID/phytree/../rvm/summary.py
VirID/phytree/../rvm/trim_contamination.py
VirID/rvm/__init__.py
VirID/rvm/anicalc.py
VirID/rvm/aniclust.py
VirID/rvm/calculate_RPM.py
VirID/rvm/histogram.py
VirID/rvm/main_taxon.py
VirID/rvm/rmdup.py
VirID/rvm/sankey.r
VirID/rvm/summary.py
VirID/rvm/trim_contamination.py
VirID/rvm/../__init__.py
VirID/rvm/../__main__.py
VirID/rvm/../assembly_and_basic_annotation.py
VirID/rvm/../cli.py
VirID/rvm/../main.py
VirID/rvm/../phylogenetic_analysis.py
VirID/rvm/../biolib/__init__.py
VirID/rvm/../biolib/common.py
VirID/rvm/../biolib/custom_help_formatter.py
VirID/rvm/../biolib/exceptions.py
VirID/rvm/../biolib/logger.py
VirID/rvm/../config/__init__.py
VirID/rvm/../config/config.py
VirID/rvm/../data/ICTV_TAXON.csv
VirID/rvm/../data/Pathogenicity_VIRUS_CSV.csv
VirID/rvm/../data/RdRP_ICTV_NR.csv
VirID/rvm/../data/__init__.py
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.csv
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.fas
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.pdf
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Astro-Poty/Astro-Poty_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.csv
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.fas
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.pdf
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Birna-Permutotetra/Birna-Permutotetra_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto.csv
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto.fas
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto.pdf
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Cysto/Cysto_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi.csv
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi.fas
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi.pdf
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Flavi/Flavi_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.csv
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.fas
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.pdf
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Hepe-Virga/Hepe-Virga_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo.csv
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo.fas
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo.pdf
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Hypo/Hypo_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.csv
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.fas
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.pdf
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Luteo-Sobemo/Luteo-Sobemo_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.csv
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.fas
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.pdf
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Narna-Levi/Narna-Levi_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.csv
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.pdf
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Bunya-Arena/Negative_Bunya-Arena_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.csv
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.pdf
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Mono-Chu/Negative_Mono-Chu_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.csv
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.pdf
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Negative_Orthomyxo/Negative_Orthomyxo_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido.csv
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido.fas
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido.pdf
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Nido/Nido_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.csv
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.fas
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.pdf
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Partiti-Picobirna/Partiti-Picobirna_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.csv
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.fas
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.pdf
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici.phylogeny.nwk
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Picorna-Calici/Picorna-Calici_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus.csv
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus.fas
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus.pdf
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Qinvirus/Qinvirus_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo.csv
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo.fas
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo.pdf
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Reo/Reo_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.csv
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.fas
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-Noda_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Tombus-Noda/Tombus-noda.pdf
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.csv
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.fas
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.pdf
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Toti-Chryso/Toti-Chryso_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus.csv
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus.fas
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus.pdf
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Weivirus/Weivirus_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus.csv
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus.fas
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus.pdf
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Yanvirus/Yanvirus_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus.csv
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus.fas
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus.pdf
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Yuevirus/Yuevirus_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.csv
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.fas
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.pdf
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/Zhaovirus/Zhaovirus_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi.csv
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi.fas
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi.pdf
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/na-daxi/na-daxi_trimmed_alignment.phy
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative.csv
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative.fas
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative.pdf
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative.phy_phyml_tree.nwk
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_info.txt
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative_RAxML_result.nwk
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.fas
VirID/rvm/../data/RdRP_tree_230328/other-negative/other-negative_trimmed_alignment.phy
VirID/rvm/../data/diamond_database/RdRP_230330_rmdup.fas
VirID/rvm/../data/diamond_database/RdRp_expanded_20230330.csv
VirID/rvm/../external/__init__.py
VirID/rvm/../external/align_trim.py
VirID/rvm/../external/blast.py
VirID/rvm/../external/fasta_process.py
VirID/rvm/../external/reads_tool.py
VirID/rvm/../external/tree_build.py
VirID/rvm/../phytree/__init__.py
VirID/rvm/../phytree/classify.py
VirID/rvm/../phytree/infectivity_distribution.r
VirID/rvm/../phytree/label_tree.r
VirID/rvm/../phytree/translate.py
VirID/rvm/../phytree/tree_taxon.py