Major Softwares   Contigs making softwares:   Phrap - Phil Green 1999, www.phrap.org   Cap3 - HUANG X, MADAN A. CAP3: A DNA sequence assembly program. Genome. Research , September 1999, vol. 9 , no. 9 p. 868-877. SSR finding Softwares:   MISA:      THIEL T., MICHALEK V. and GRANER A. Exploiting EST data-bases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and .Applied Genetics . February 2003 Vol 106 no.3,p. 411–422. TRA:      BILGEN M, KARACA M, ONUS A and INCE A. A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. Bioinformatics. July 15 , 2004 , Vol. 20 , no. 18 p. 3379-3386.   SSRIT:      Temnykh-S, DeClerck-G, Lukashova-A, Lipovich-L, Cartinhour-S, McCouch-S, Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential . Genome Research August 2001,Vol. 11, Issue 8, p.1441-1452. SSRPRIMER:      ROBINSON AJ, LOVE CG, BATLEY J, BARKER G and EDWARDS D. Simple Sequence Repeat Marker Loci Discovery using SSR Primer. Bioinformatics . February 2004 Vol. 20 p. 1475 – 1476 . SNP Detecting Softwares: Auto SNP:      BARKER, G., BATLEY, J., O'SULLIVAN, H., EDWARDS,K.J, and EDWARDS, D. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics , 2003, vol. 19, p. 421-422.