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  • Happlot - Haplotype diagram plotting

    Sample In | Sample Out | Download (46.1 KB Zip File)
    Instructions

    HAPPLOT reads a list of polymorphic sites and their locations in a collection of DNA sequences and creates a postscript file diagramming the site locations. HAPPLOT uses the output file from PSFIND as the input file.

    Example input polymorphic sites file (.psi) data is flic6.ps:

    FliC_6  test data set                   
    
     Total seq length =  1650
     No. alleles       =    6
     Polymorphic sites =  678
    
     Allele labels
        1  H6_DEC1a            
        2  H6_DEC2a            
        3  H6_E851             
        4  H7_DEC3a            
        5  H7_DEC13A           
        6  H7_O1               
    
     Site  Loc  C   2   4   6
        1    20 G . . . . T .
        2    73 G . . . . T .
        3    78 G . . . A A .
        4   132 T . . . G . .
        5   135 A . . . C . .
        6   165 A . . . G G .
        7   168 G A . . . A .
        8   174 C T T T . . .
        9   189 C . . . . . T
    10	216 C . . . T T .
    11	..
    
    and so forth for 678 sites
    
    Output file

    The postscript output file (use extension .ps) can be converted to a pdf file by Acrobat Distiller or it can be imported into graphics programs such as Adobe Illustrator or Micrographics designer.

    Contact stec@cvm.msu.edu
    Operated by Shannon D. Manning at Michigan State University