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  • PS Win - Sliding window of site differences

    Sample In | Sample Out | Download (34.2 KB Zip File)
    Instructions

    His program tabulates the proportion of synonymous and non-synonymous sites (by Nei and Gojobori's 1986 method, Mol. Biol. Evol. 3:418-426) for a specified number of codons in a sliding window. The program reads a table called codon.tab, which must be in the same folder where the executable resides. The output is the percentage of synonymous sites (pS x 100) and non-synonymous sites (pN x 100) calculated for each window.

    First set up your input sequence file using notepad. Copy and paste the sequences from Editseq or other file format. The input file must have the following format:

    Line 1 		title
    Line 2 		allele name (OTU name)
    Line 3 and on	Sequence in upper case letters
    A,T,C,G,N (missing data), and '-' for deletions
    sequence must end with ;
    Later Line 		next allele name
    Later line +1 	next sequence, end in ;
    And so forth
    

    Example sequence data are in the file mdh6.txt

    Make sure there should be no blank lines after the last semicolon.

    Default parameters for PSWIN are:

    MXB=6000    maximum number of bases per sequence
    MXSQ=50     maximum number of sequences (OTUs)
    MXAA=2000   maximum number of codon positions
    

    To execute

    Start the command prompt and go to the directory with your input sequence file. Type 'pswin' and respond to queries.

    You can also copy pswin.exe to your data folder; however, in this case, you must also copy codon.tab to the same folder. Go to your folder and click on pswin to execute.

    Output

    The output file lists the ps x 100 and pn x 100 values for each position in the sequence. The position is listed as the middle codon of the specified window size. This list can be pasted into Excel to create a sliding window plot along the entire sequence.

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