https://github.com/JosephCrisp/NewZealand_Tools
History
Tip revision: ecf350e997c5e0f960398a398ee0be333c457d8c authored by JosephCrisp on 08 August 2016, 10:51:04 UTC
Add files via upload
Tip revision: ecf350e
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AddCladeToIsolateTraitsFile_22-07-16.pl -rw-r--r-- 1.8 KB
AddSamplingInfoToPhylipMLTree.pl -rw-r--r-- 2.6 KB
CalculateGeneticDistances_01-06-16.pl -rw-r--r-- 3.4 KB
CalculateGeneticDistances_FilterSensitivity_10-06-16.jar -rw-r--r-- 12.2 MB
CombineSampleInfoIntoSingleFile.pl -rw-r--r-- 5.5 KB
ConvertBranchLengthsToSNPs_07-07-16.pl -rw-r--r-- 8.8 KB
ConvertBranchLengthsToSNPs_22-07-16.pl -rw-r--r-- 8.8 KB
ConvertFasta2Nexus_14-06-16.pl -rw-r--r-- 14.8 KB
ConvertFasta2Phylip.pl -rw-r--r-- 2.7 KB
CreateFastaFromFiltered_13-06-16.pl -rw-r--r-- 7.9 KB
CreateFastaWithReferenceFromFiltered_03-05-16.pl -rw-r--r-- 7.5 KB
CreateRandomWildlifeCattlePairsFiles_23-06-16.sh -rw-r--r-- 1.3 KB
CreateTipRandomisationFiles_23-06-16.sh -rw-r--r-- 1.2 KB
ExamineBLASTOutput.pl -rw-r--r-- 3.0 KB
ExamineGeneticDistanceClustering_16-06-16.R -rw-r--r-- 4.1 KB
ExamineGeneticDistanceClustering_21-07-16.R -rw-r--r-- 4.2 KB
ExamineGenomeCoverage_06-06-16.pl -rw-r--r-- 6.4 KB
FilterSensitivityAnalysis_NewZealand_01-06-16.sh -rw-r--r-- 4.3 KB
FilterVariants.pl -rw-r--r-- 9.3 KB
FilterVariants_14-06-16.pl -rw-r--r-- 10.0 KB
FindColouredCladesInFigtreeFile.pl -rw-r--r-- 2.6 KB
FindSpatiallyAndTemporallyMatchedPairs.pl -rw-r--r-- 9.5 KB
FitRandomForestModelForFilterSensitivityAnalysis_01-06-16.R -rw-r--r-- 2.9 KB
GenerateEpiVariables_NewZealand_01-06-16.pl -rw-r--r-- 5.7 KB
GenerateFilters_01-06-16.pl -rw-r--r-- 1.1 KB
KeepCladeInFasta_07-07-16.pl -rw-r--r-- 3.6 KB
KeepCladeInMerged_01-06-16.pl -rw-r--r-- 3.1 KB
KeepMatchedIsolatesInFasta_15-06-16.pl -rw-r--r-- 3.6 KB
MergeVCFFiles_23-05-16.jar -rw-r--r-- 12.2 MB
NoteSelectedIsolatesFromAllIsolates_22-07-16.pl -rw-r--r-- 1.7 KB
PickRandomReadsFromSAM.pl -rw-r--r-- 2.4 KB
PlotFilterSensitivityOutput_13-06-16.R -rw-r--r-- 6.1 KB
PlotSamplingLocations_22-07-16.R -rw-r--r-- 2.6 KB
PlotSpatiallyAndTemporallyMatchedIsolates.R -rw-r--r-- 2.6 KB
PlotStateTransitionRateEstimations_28-07-16.R -rw-r--r-- 38.3 KB
PlotSubstitutionRate_21-07-16.R -rw-r--r-- 26.8 KB
PlotTemporalRangeOfClades_22-07-16.R -rw-r--r-- 3.8 KB
PlotTipRandomisationSubstitutionRateEstimations_21-07-16.R -rw-r--r-- 6.1 KB
Plot_Path-o-gen_Data_08-07-16.R -rw-r--r-- 6.8 KB
README.md -rw-r--r-- 158 bytes
RandomlySelectWildlifeAndCattle_23-06-16.pl -rw-r--r-- 4.9 KB
RandomlyShuffleYearsInNexus_23-06-16.pl -rw-r--r-- 4.0 KB
RemoveUninformativeSites_13-06-16.pl -rw-r--r-- 4.9 KB
test.pl -rw-r--r-- 510 bytes

README.md

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