├── HaploABBABABA_multithreaded.jar ├── Phix_Removal.sh ├── README.md ├── addRecombRates.r ├── allelicBalance.py ├── convertIndsFineSTR.sh ├── convertVCFtoEigenstrat.sh ├── createRADmappingReport.sh ├── createuniformrecmap.r ├── demultiplexing.sh ├── filter_vcf.py ├── ldPruning.sh ├── makeRecombMap4fineSTRUCTURE.sh ├── makeRelateMap.r ├── removeNonsignDsuite.r ├── runBowtie2RADID.sh ├── vcf2fineRADstructure.sh ├── vcf2fineSTR.lsf └── vcf2phylip.py /HaploABBABABA_multithreaded.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/joanam/scripts/HEAD/HaploABBABABA_multithreaded.jar -------------------------------------------------------------------------------- /Phix_Removal.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/joanam/scripts/HEAD/Phix_Removal.sh -------------------------------------------------------------------------------- /README.md: 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