CheckAlign 2.0 is freely available as both a standalone application (a) and as an online server version (b).

(a) The software has been designed as an open source and distributed in two versions: a Java package (jar) compatible with all platforms and a self-installable executable package for Microsoft Windows platforms.

(b) The server version is available as a PHP script and requires an HTTP web server. Therefore you make sure that a web server engine and a PHP application server are properly installed on your system. This version also allows users to generate hidden Markov model (HMM) profile and consensus sequences based on the alignments under analysis (this implementation is not included into the software version).


The CheckAlign 2.0 standalone application is distributed as an installer for Windows XP/Vista/7 (32 bit and 64 bit), a self-extracting disk image for Mac OS X 10.5 or later (64 bit), and a compressed tarball archive for Linux 2.6 kernel series or later (32 bit and 64 bit).


The standalone application requires Java 6 or later. The minimum system requirements for this software are a PC with a Pentium 4 1.5 GHz or AMD Athlon XP 1500+ processor or higher with at least 1 GB of RAM.

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