/PolarizePigAncestralAlleles

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PolarizePigAncestralAlleles

This repository is deposited with scripts for polarization of ancestral alleles of pig reference genome (Sscrofa11.1).
The report has been prepared for submission.

  • Genome_Alignment_Scripts
    The Genome_Alignment_Scripts directory includes the scripts of Progressive Cactus pipeline to align reference genomes together and deposit results in HAL format. The HAL format file is converted into MAF format with Sscrofa11.1 as reference.
    Then the reconstructed ancestral sequences of pig, Sus, and Suidae are exported.
    The Linux Shell scripts should be run in order 01, 02, 03. The other scripts and files will be automatically called by .sh scripts for running.

  • Rscript_to_Validate_AA_byMP_inSplitChr.R
    The R script Rscript_to_Validate_AA_byMP_inSplitChr.R is used to perform the polarization via the major alleles of suids at a locus. The polarization is based on three representative outgroup species and a maximum-parsimony principle.
    The corresponding details have been listed in the script.