Files in thednainus/pangeaZA

Analyses and models for PANGEA data from South Africa (ZA).

Analyses/Scripts/Python-scripts/.idea/Python-scripts.iml

Analyses/Scripts/Python-scripts/.idea/dictionaries/user.xml

Analyses/Scripts/Python-scripts/.idea/encodings.xml

Analyses/Scripts/Python-scripts/.idea/misc.xml

Analyses/Scripts/Python-scripts/.idea/modules.xml

Analyses/Scripts/Python-scripts/.idea/workspace.xml

Analyses/Scripts/Python-scripts/blast_source_sequences_pangea.py

Analyses/Scripts/Python-scripts/getGenBank.py

Analyses/Scripts/Python-scripts/get_source_IDs.py

Analyses/Scripts/Python-scripts/miscellaneous.py

Analyses/Scripts/R-scripts/South_Africa/1.1_SA_getting_data_part1.R Analyses/Scripts/R-scripts/South_Africa/1.2_SA_getting_data_part2.R Analyses/Scripts/R-scripts/South_Africa/2_SA_subtyping.R Analyses/Scripts/R-scripts/South_Africa/3_SA_convert_PANGEA_toFASTA.R Analyses/Scripts/R-scripts/South_Africa/4_SA_get_CGR_PANGEA.R Analyses/Scripts/R-scripts/South_Africa/5_SA_remove_drugResistance.R Analyses/Scripts/R-scripts/South_Africa/6_get_missingJob_numbers.R Analyses/Scripts/R-scripts/South_Africa/Summary.R Analyses/Scripts/R-scripts/South_Africa/env.R Analyses/Scripts/R-scripts/South_Africa/gag.R Analyses/Scripts/R-scripts/South_Africa/get_SA_data.R Analyses/Scripts/R-scripts/South_Africa/pol.R Analyses/Scripts/R-scripts/South_Africa/treedater_env.R Analyses/Scripts/R-scripts/South_Africa/treedater_env_boot.R Analyses/Scripts/R-scripts/South_Africa/treedater_gag.R Analyses/Scripts/R-scripts/South_Africa/treedater_gag_boot.R Analyses/Scripts/R-scripts/South_Africa/treedater_pol.R Analyses/Scripts/R-scripts/South_Africa/treedater_pol_boot.R

Analyses/Scripts/bash-scripts/ML_script.sh

Analyses/Scripts/bash-scripts/bootstrap_script.sh

DESCRIPTION

NAMESPACE

R/mcmcFit0.R R/misc.R R/model0.R R/model0summary.R R/remove_redundant_cgr.R R/treedater0.R R/treestructure0.R README.md man/generate_model0.Rd man/get_sequences.Rd man/getsubtres.Rd man/getsubtresRecursively.Rd man/m0R.t.Rd man/mcmcfit0.0.Rd man/root_and_drop_tips.Rd man/rrcgr.Rd man/rrcgr2.Rd man/sa_treedater.Rd man/setup.model.equations.Rd man/summary_model0.Rd man/trajectories_model0.Rd

pangeaZA.Rproj

thednainus/pangeaZA documentation built on May 9, 2022, 6:21 p.m.