Data and scripts used in DCC clade emergence manuscript
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The data within the data folder are: alignments - contains alignments for each FastBAPS cluster. Named as subspecies_clusterNumber so abscessus_2.fasta is the alignment for abscessus subspecies FastBAPS cluster 2
BEAST_log_files - output log files from BEAST for DCC phylogeography runs. All are combined from at least 3 independent runs and have had burnin removed so all states in these files were used in analyses. These files are: DCC1.log - informed substitution rate prior from TempEst analysis, no phylogeography. Used to reconstruct temporal and population history DCC1_uniform.log - uniform substitution rate prior between 10^-5 and 10^-9, no phylogeography DCC1_date_randomisation1.log - dates randomised, uniform substitution rate prior. Used for date randomisation test DCC1_phylogeography.log - asymmetric phylogeography DCC1_phylogeography_sample1.log - asymmetric phylogeography with over-represented continents downsampled. 5 subsamples from each of DCC1, DCC2 and DCC3
BEAST_XMLs - XML files used in BEAST analyses. These files are: DCC1.xml - informed substitution rate prior from TempEst analysis, no phylogeography. Used to reconstruct temporal and population history DCC1_uniform.xml - uniform substitution rate prior between 10^-5 and 10^-9, no phylogeography DCC1_date_randomisation1.xml - dates randomised, uniform substitution rate prior. Used for date randomisation test DCC1_phylogeography.xml - asymmetric phylogeography DCC1_phylogeography_sample1.xml - asymmetric phylogeography with over-represented continents downsampled. 5 subsamples from each of DCC1, DCC2 and DCC3
clade_age_versus_continents - all of the clades in the DCC phylogeographic trees with their age and number of descendent continents
DCC_Bayesian_skyline_plots - Bayesian skyline plot estimates of relative genetic diversity through time for each DCC
DCC_expansion_distributions - first expansion dates in each tree in the posterior distribution for each DCC
mutational_spectra - counts of context-specific mutations used in mutational spectrum analyses. non_DCC_internal_spectrum.csv is the mutation counts for the non-DCC internal branches. DCC_internal_spectrum.csv is the mutation counts for the DCC internal branches. within_CF_patient_spectrum.csv is the mutation counts for within CF patient mutations. signature_proportions.xlsx contains the proportion of mutations assigned to each mutational signature by signal for each dataset
other_data smoking_data.csv - trends in cigarette sales through time for a set of countries CF_survival.csv - life expectancy of individuals with Cystic Fibrosis through time
phylogeographic_trees - maximum clade credibility trees for DCCs 1-3 with phylogeographic reconstructions
sequence_metadata - metadata for all sequences included in the study
SNP_distances - the minimum number of SNPs between isolates from all patients with isolates in the same FastBAPS cluster
temporal_trees - BEAST maximum clade credibility trees for each DCC. dcc_substitution_rates.xlsx contains the inferred substitution rates for DCCs 1-4
trees - phylogenetic trees for each FastBAPS cluster
The scripts in the scripts folder are: mutationalSpectrum.v1.py - used to reconstruct the mutational spectrum from a PAML rst file
combineMutationalSpectra.R - combines multiple mutational spectra into a single spectrum
bootstrapMutationSpectrum.R - calculates the significance of differences in mutational spectra using a permutation test
plotSpectrum.R - plots a mutational spectrum
plotMCCTrees.R - plots a MCC tree coloured by inferred location
mapDCCMigrationsMap.R - plots supported DCC migration rates on a world map
plotTransmissionNetwork.R - plots a transmission network at a given SNP cutoff
extractPopulationIncrease.py - used to extract the dates of increases in relative genetic diversity from a posterior distribution of trees