LICENSE
MANIFEST.in
README.md
setup.py
ERVsearch/Bed.py
ERVsearch/ERVsearch
ERVsearch/ERVsearch.py
ERVsearch/Errors.py
ERVsearch/Exonerate.py
ERVsearch/Fasta.py
ERVsearch/HelperFunctions.py
ERVsearch/ORFs.py
ERVsearch/Regions.py
ERVsearch/Summary.py
ERVsearch/Trees.py
ERVsearch/__init__.py
ERVsearch/_version.py
ERVsearch/ERV_db/all_ERVs_aa.fasta
ERVsearch/ERV_db/all_ERVs_nt.fasta
ERVsearch/ERV_db/convert.tsv
ERVsearch/ERV_db/env.fasta
ERVsearch/ERV_db/gag.fasta
ERVsearch/ERV_db/pol.fasta
ERVsearch/ERV_db/.ipynb_checkpoints/Untitled-checkpoint.ipynb
ERVsearch/phylogenies/outgroups.tsv
ERVsearch/phylogenies/group_phylogenies/ALV-like_alpha_gag.fasta
ERVsearch/phylogenies/group_phylogenies/ALV-like_alpha_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Avian_alpha_gag.fasta
ERVsearch/phylogenies/group_phylogenies/Avian_alpha_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Avian_beta_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Avian_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/ERVL-like_spuma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/FIV1_lenti_env.fasta
ERVsearch/phylogenies/group_phylogenies/FIV1_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/FIV2_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/FIV_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/Fish-Amphibian1_epsilon_pol.fasta
ERVsearch/phylogenies/group_phylogenies/FishAmphibian1_epsilon_pol.fasta
ERVsearch/phylogenies/group_phylogenies/FishReptile1_epsilon_pol.fasta
ERVsearch/phylogenies/group_phylogenies/GALV-like_gamma_env.fasta
ERVsearch/phylogenies/group_phylogenies/GALV-like_gamma_gag.fasta
ERVsearch/phylogenies/group_phylogenies/GALV-like_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/HERVF-like_gamma_gag.fasta
ERVsearch/phylogenies/group_phylogenies/HERVI-like_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/HERVK-like_beta_env.fasta
ERVsearch/phylogenies/group_phylogenies/HERVK-like_beta_gag.fasta
ERVsearch/phylogenies/group_phylogenies/HERVK-like_beta_pol.fasta
ERVsearch/phylogenies/group_phylogenies/HERVR-like_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/HIV_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/IAP-like_beta_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Jaagsieke-like_beta_env.fasta
ERVsearch/phylogenies/group_phylogenies/Jaagsieke-like_beta_gag.fasta
ERVsearch/phylogenies/group_phylogenies/Jaagsieke-like_beta_pol.fasta
ERVsearch/phylogenies/group_phylogenies/MLV-like_gamma_env.fasta
ERVsearch/phylogenies/group_phylogenies/MLV-like_gamma_gag.fasta
ERVsearch/phylogenies/group_phylogenies/MLV-like_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Mustelidae_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/Non-Simian-Foamy_spuma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/REV-like_gamma_gag.fasta
ERVsearch/phylogenies/group_phylogenies/REV-like_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Reptiles1_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Reptiles2_gamma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Rodent-Syncytin_gamma_env.fasta
ERVsearch/phylogenies/group_phylogenies/SIV1-HIV_lenti_env.fasta
ERVsearch/phylogenies/group_phylogenies/SIV1_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/SIV1_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/SIV2-HIV_lenti_env.fasta
ERVsearch/phylogenies/group_phylogenies/SIV2-HIV_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/SIV2-HIV_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/SIV3_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/SRV-like_beta_env.fasta
ERVsearch/phylogenies/group_phylogenies/SRV-like_beta_gag.fasta
ERVsearch/phylogenies/group_phylogenies/SRV-like_beta_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Simian-Foamy-1_spuma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Simian-Foamy-2_spuma_pol.fasta
ERVsearch/phylogenies/group_phylogenies/Simian-Syncytin_gamma_env.fasta
ERVsearch/phylogenies/group_phylogenies/Visna-like_lenti_env.fasta
ERVsearch/phylogenies/group_phylogenies/Visna-like_lenti_gag.fasta
ERVsearch/phylogenies/group_phylogenies/Visna-like_lenti_pol.fasta
ERVsearch/phylogenies/group_phylogenies/WDSV-like_epsilon_pol.fasta
ERVsearch/phylogenies/group_phylogenies/env_alpha.fasta
ERVsearch/phylogenies/group_phylogenies/env_beta.fasta
ERVsearch/phylogenies/group_phylogenies/env_delta.fasta
ERVsearch/phylogenies/group_phylogenies/env_epsilon.fasta
ERVsearch/phylogenies/group_phylogenies/env_gamma.fasta
ERVsearch/phylogenies/group_phylogenies/env_lenti.fasta
ERVsearch/phylogenies/group_phylogenies/env_spuma.fasta
ERVsearch/phylogenies/group_phylogenies/gag_alpha.fasta
ERVsearch/phylogenies/group_phylogenies/gag_beta.fasta
ERVsearch/phylogenies/group_phylogenies/gag_delta.fasta
ERVsearch/phylogenies/group_phylogenies/gag_epsilon.fasta
ERVsearch/phylogenies/group_phylogenies/gag_gamma.fasta
ERVsearch/phylogenies/group_phylogenies/gag_lenti.fasta
ERVsearch/phylogenies/group_phylogenies/gag_spuma.fasta
ERVsearch/phylogenies/group_phylogenies/pol_alpha.fasta
ERVsearch/phylogenies/group_phylogenies/pol_beta.fasta
ERVsearch/phylogenies/group_phylogenies/pol_delta.fasta
ERVsearch/phylogenies/group_phylogenies/pol_epsilon.fasta
ERVsearch/phylogenies/group_phylogenies/pol_gamma.fasta
ERVsearch/phylogenies/group_phylogenies/pol_lenti.fasta
ERVsearch/phylogenies/group_phylogenies/pol_spuma.fasta
ERVsearch/phylogenies/summary_phylogenies/env_alpha.fasta
ERVsearch/phylogenies/summary_phylogenies/env_alpha_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_beta.fasta
ERVsearch/phylogenies/summary_phylogenies/env_beta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_delta.fasta
ERVsearch/phylogenies/summary_phylogenies/env_delta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_epsilon.fasta
ERVsearch/phylogenies/summary_phylogenies/env_epsilon_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_gamma.fasta
ERVsearch/phylogenies/summary_phylogenies/env_gamma_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_lenti.fasta
ERVsearch/phylogenies/summary_phylogenies/env_lenti_A.fasta
ERVsearch/phylogenies/summary_phylogenies/env_spuma.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_alpha.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_alpha_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_beta.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_beta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_delta.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_delta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_epsilon.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_epsilon_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_gamma.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_gamma_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_lenti.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_lenti_A.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_spuma.fasta
ERVsearch/phylogenies/summary_phylogenies/gag_spuma_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_alpha.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_alpha_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_beta.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_beta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_delta.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_delta_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_epsilon.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_epsilon_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_gamma.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_gamma_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_lenti.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_lenti_A.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_spuma.fasta
ERVsearch/phylogenies/summary_phylogenies/pol_spuma_A.fasta
ERVsearch/templates/pipeline.ini
ervsearch.egg-info/PKG-INFO
ervsearch.egg-info/SOURCES.txt
ervsearch.egg-info/dependency_links.txt
ervsearch.egg-info/requires.txt
ervsearch.egg-info/top_level.txt
man/Makefile
man/conf.py
man/contents.rst
man/index.rst
man/make.bat
man/_build/doctrees/contents.doctree
man/_build/doctrees/environment.pickle
man/_build/doctrees/index.doctree
man/_build/doctrees/pages/ERVregions.doctree
man/_build/doctrees/pages/classify.doctree
man/_build/doctrees/pages/functions.doctree
man/_build/doctrees/pages/introduction.doctree
man/_build/doctrees/pages/outputs.doctree
man/_build/doctrees/pages/parameters.doctree
man/_build/doctrees/pages/screen.doctree
man/_build/html/.buildinfo
man/_build/html/contents.html
man/_build/html/genindex.html
man/_build/html/index.html
man/_build/html/objects.inv
man/_build/html/search.html
man/_build/html/searchindex.js
man/_build/html/_images/pipeline.png
man/_build/html/_sources/contents.rst.txt
man/_build/html/_sources/index.rst.txt
man/_build/html/_sources/pages/ERVregions.md.txt
man/_build/html/_sources/pages/classify.md.txt
man/_build/html/_sources/pages/functions.md.txt
man/_build/html/_sources/pages/introduction.md.txt
man/_build/html/_sources/pages/outputs.md.txt
man/_build/html/_sources/pages/parameters.md.txt
man/_build/html/_sources/pages/screen.md.txt
man/_build/html/_static/alabaster.css
man/_build/html/_static/basic.css
man/_build/html/_static/custom.css
man/_build/html/_static/doctools.js
man/_build/html/_static/documentation_options.js
man/_build/html/_static/file.png
man/_build/html/_static/jquery-3.5.1.js
man/_build/html/_static/jquery.js
man/_build/html/_static/language_data.js
man/_build/html/_static/minus.png
man/_build/html/_static/plus.png
man/_build/html/_static/pygments.css
man/_build/html/_static/searchtools.js
man/_build/html/_static/underscore-1.3.1.js
man/_build/html/_static/underscore.js
man/_build/html/_static/css/badge_only.css
man/_build/html/_static/css/theme.css
man/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff
man/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2
man/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff
man/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2
man/_build/html/_static/css/fonts/fontawesome-webfont.eot
man/_build/html/_static/css/fonts/fontawesome-webfont.svg
man/_build/html/_static/css/fonts/fontawesome-webfont.ttf
man/_build/html/_static/css/fonts/fontawesome-webfont.woff
man/_build/html/_static/css/fonts/fontawesome-webfont.woff2
man/_build/html/_static/css/fonts/lato-bold-italic.woff
man/_build/html/_static/css/fonts/lato-bold-italic.woff2
man/_build/html/_static/css/fonts/lato-bold.woff
man/_build/html/_static/css/fonts/lato-bold.woff2
man/_build/html/_static/css/fonts/lato-normal-italic.woff
man/_build/html/_static/css/fonts/lato-normal-italic.woff2
man/_build/html/_static/css/fonts/lato-normal.woff
man/_build/html/_static/css/fonts/lato-normal.woff2
man/_build/html/_static/js/badge_only.js
man/_build/html/_static/js/html5shiv-printshiv.min.js
man/_build/html/_static/js/html5shiv.min.js
man/_build/html/_static/js/theme.js
man/_build/html/pages/ERVregions.html
man/_build/html/pages/classify.html
man/_build/html/pages/functions.html
man/_build/html/pages/introduction.html
man/_build/html/pages/outputs.html
man/_build/html/pages/parameters.html
man/_build/html/pages/screen.html
man/images/pipeline.png
man/images/pipeline.svg
man/pages/functions.md
man/pages/introduction.md
man/pages/outputs.md
man/pages/parameters.md