Scripts used for data analysis in the MHC introgression project
- AmpliSAS_running/ - scripts used to run AmpliSAS software
- AmpiSAS_resultAnalysis/ - scripts used to analyse AmpliSAS outputs
- BLASTing/ - scripts used to run and analyse BLAST searches
- short_simple_specific/ - simple scripts created to perform short and specific tasks
- hzar_wrapper/ - scripts used to fit and analyse geographic clines with hzar package
- genomicClines/ - script used to fit genomic clines with ML method and gather their 2LL intervals
- Direct_analysis_MHCintrogression/ - scripts and data used to analyse MHC introgression
- build_circular_tree.R - Draws circular tree of DNA sequences - filters sequences, aligns sequences, builds tree, draws circular tree
- MHC_allele_sharing_with_permutations_TG_SES.py - modified prof. Babik's script performing permutation test for increased sharing of MHC alleles in parapatry.
- primers_design_MHC.py - script to design multiple primers for highly variable regions (e.g. MHC)
- raw_mapping.py - perform mapping of raw reads to reference sequences using bowtie2
- sra.tool.py - download raw reads from SRA based on the text file with accessions
- perform STRUCTURE analysis in parallel
- trinity_tool.py - creates de novo RNA assembly using Trinity software