├── .DS_Store ├── .Rapp.history ├── .gitignore ├── ClustInput ├── Maxxa.txt ├── TX2094.txt └── repStruc.txt ├── LICENSE ├── PCAanalysis.r ├── QTL.r ├── README.md ├── analysis ├── Collinear_Orthologs │ ├── .4_MCScan_OrthoFinder_overlap.py.swp │ ├── 1_Orthofinder_blast_uncode.py │ ├── 2_Orthofinder_orthologs_from_tandems.py │ ├── 3_Orthofinder_singletons_from_MCScanXh.py │ ├── 4_MCScan_OrthoFinder_overlap.py │ ├── 5_CheckTandems.py │ ├── 6_Orthofinder_to_all_pairwise.py │ ├── GroupSizeTable_Orthofinder.py │ ├── MCScan_OrthoFinder_overlap.py │ ├── README.md │ └── Singletons_to_pairwise.py └── TxMx_gatk │ └── gatk.sh ├── boxplotByCategory.dev.r ├── boxplotByCategory.r ├── checkCistran.by.cutoff.pdf ├── cistrans.deseq2.r ├── cistrans.fraser.r ├── cistrans.pre.r ├── coexpressionNet.r ├── compareHomoeologs.r ├── compareReciprocalF1s.r ├── countTables ├── MaxxaAlleleReadCounts.txt ├── TX2094AlleleReadCounts.txt ├── readme.txt └── totalReadCounts.txt ├── exclude ├── RSAT.md ├── TFDBscan.r ├── 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