NJtandem: a Neighbor Joining Approach for Reconstructing Tandem Duplication History

Tandem repeats, which consist of two or more contiguous copies of a particular pattern of nucleotides, are a major group of repeats in genomes. Tandem repeats are believed to have arisen from tandem duplications, in which a stretch of DNA (which may contain several repeating patterns) is transformed into two adjacent copies. Reconstructing duplication histories for tandem repeats may yield valuable insights into their functions and the biological mechanisms of their creation and extension.
NJtandem is a program to reconstruct tandem duplication history, using a neighbor-joining approach. Please see our paper A Neighbor Joining Approach for Reconstructing Tandem Duplication History for details.


download source files

download executable for Windows

download executable for Unix (complied under Sun Solaris)
 
How to Use NJtandem

If UNIX executable is downloaded, it needs to be decompressed first.
Please use the following two commands in order to decompress.
  (1) gunzip NJtandem.tar.gz
  (2) tar xvf NJtandem.tar
Now you get a file named NJtandem, which can be executed directly.

To execute the program, simply type NJtandem.
The program will ask you to input a file name, indicate whether it contains protein or DNA sequences, and choose an algorithm.
Here is a sample input file, which contains 17 repeats in MUC5B.

The program generates an evolutionary tree and outputs a string representation of the tree, as well as duplication blocks of the tree.