2007-11: A new version of INAASE.

November 2007 – A new version of INAASE (INtegration of Ambiguously Aligned SEquences).

Since it’s inception, INAASE (a program developed for the integration of ambiguously aligned sequences into phylogenetic analyses) has been an important tool for revealing signal in gaps and hypervariable regions. In the newest version, an interface has made it more user-friendly, and the alignment algorithm has been significantly improved. Here you will find the most recent version of
INAASE (3.0; ZIP file). It has been tested on Mac OSX, Windows XP and Linux (Debian 4.0, desktop version, but any other distro should also work). Please note that it works only with Java 1.5 or higher installed.

Lutzoni, F., Wagner, P., Reeb V., and Zoller, S. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49:628-651.
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