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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
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.
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.