Dina workshop: Java biosequence alignment applet

Another page demonstrates construction and drawing of phylogenetic trees.

The alignment program

E.g., try the example sequences HEAGAWGHEE and PAWHEAE:

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Notes

• This version includes Global, Local, Affine Global, Smart Global, and Smart Affine Local alignment.
• The linear gap cost algorithms charge 8*k for a gap of length k.
• The affine gap cost algorithms charge 10+2*k for a gap of length k.
• You may use letters from the alphabet ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv.
• All other characters are ignored, including spaces etc.
• To copy sequences from other web pages, mark them using the mouse, press Ctrl+C, point at a textfield in the applet, and press Ctrl+V.
• The value -Inf means minus infinity.
• To print the contents of the textarea, select the text, copy it to a text editor (e.g. WordPad) and print it from there, preferably using a fixed-width font such as Courier.

Links

• Some lecture slides from a Dina Research School workshop.
• A description of the implementation, and some more algorithms.
• The program source code
• The additional applet user interface source code

Note that Microsoft Windows suffers from a limitation: a browser applet text component can contain only approx. 50,000 characters; all excess characters are discarded. This is not a limitation of this program, of Java, or of Netscape.