├── .gitignore ├── LICENSE ├── README.md ├── example ├── IDlist.txt ├── globalPercentID_CDS.txt ├── listPhenotype.txt ├── localPercentID_CDS.txt ├── output.txt └── tree_ancestor.nh ├── forwardGenomics.R ├── forwardGenomics_fullAnalysis.R ├── forwardGenomics_globalAnalysis.R ├── forwardGenomics_initialization.R ├── forwardGenomics_localAnalysis.R ├── lookUpData ├── branchWeights_CDS.txt ├── branchWeights_CNE.txt ├── expPercentID_CDS.txt └── expPercentID_CNE.txt └── scripts ├── Assembly2Species.perl ├── ConvertFastaToFastaOneLine.perl ├── ConvertTreeModToNewick.perl ├── GetGlobalAndLocalPercentID.perl ├── Globals.pm ├── Maf2SpanningSeq_PRANK.perl ├── MyBDB.pm ├── MyKentFunctions.pm └── ReadBDB.perl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hillerlab/ForwardGenomics/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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