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  • Death by Genomic Sudoku

    I am a grad student with Promethean aspirations, and the challenges that come with such an undertaking.

    I have 154 chromatograms of heterozygous reptile DNA (did I really choose Population Genetics?...oops).

    I am using Sequencher to process and feel like I am using caveman sudoku techniques to bang my head on the cave wall. The problem is determining from which parent a peak has come and determining which nucleotide to select in ambiguities...accounting for insertions and deletions as well. This can take days-of-hours for each chromatogram and I am out of undergrads (they really don't have the aptitude).

    I am looking for tools that will, optimally, detect the deletions, and determine from whom each ambiguous nucleotide originated. Less optimally, but still appreciated, would be a tool that will find me the easy and/or obvious answers I need and also show what the likely insetions and deletions are so that I can have a somewhat better place to start with Human trial-and-error analysis.

    Thank you if you can help,

    ThePhyxr

  • #2
    Not sure if you have run across MEGA as yet. http://megasoftware.net/

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