DAMBE (Software package for extensive data analysis in molecular biology and evolution, for Windows ME/2000/XP/VISTA and Linux)
AMIADA (Analyzing Microarray Data, for Windows ME/2000/XP/VISTA)
goldMINER (for automated gene annotation and functional classification by using local and remote searches against databases of protein functional classification such as pFAM, CDD, etc.)
Books related to the software
Xia, X. 2007. Bioinformatics and the cell: modern
computational approaches in genomics, proteomics and transcriptomics. Springer.
361 pp. Find the book in a library near you.