Motivation: Genomes are replete with short sequences repeated consecutively called tandem repeats. Reconstructing duplication histories for tandem repeats may yield valuable insights into their functions and the biological mechanisms of tandem repeat creation and extension. Results: we design and implement a set of heuristic algorithms for reconstructing tandem duplication history with neighbor...

Motivation: Genomes are replete with short sequences repeated consecutively called tandem repeats. Reconstructing duplication histories for tandem repeats may yield valuable insights into their functions and the biological mechanisms of tandem repeat creation and extension. Results: We study the generalized neighbor-joining approaches for reconstructing tandem duplication history. We develop a ...

Plants have substantially higher gene duplication rates compared with most other eukaryotes. These plant gene duplicates are mostly derived from whole genome and/or tandem duplications. Earlier studies have shown that a large number of duplicate genes are retained over a long evolutionary time, and there is a clear functional bias in retention. However, the influence of duplication mechanism, p...

Plants have substantially higher gene duplication rates compared with most other eukaryotes. These plant gene duplicates are mostly derived from whole genome and/or tandem duplications. Earlier studies have shown that a large number of duplicate genes are retained over a long evolutionary time, and there is a clear functional bias in retention. However, the influence of duplication mechanism, p...