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Using the Alignment Editor you can also create a distance matrix of a multiple sequence alignment.

To create a distance matrix, use the Statistics ‣ Generate distance matrix item in the Actions main menu or in the context menu.

The dialog will appear:

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     <img src="/wiki/download/attachments/7667753/Distance Matrix.png"/>
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The following parameters are available:

Distance algorithm - there are two distance algorithms: "Hamming distance" for dissimilarity and "Simple similarity" for similarity.

Profile mode: Counts/Percents — select the Percents to have scores shown as percents in the report. Also you can Exclude gaps.

Show group statistics of multiple alignment - shows group statistics when the collapsing is switched on.

Save profile to file — allows to save profile to a file in the HTML or CSV format. The CSV format is convenient for further processing in worksheets editors like Excel.

The result profile in the HTML mode:

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     <img src="/wiki/download/attachments/7667753/Distance Matrix_1.png"/>
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