Sequence Alignment

• USC Sequence Alignment Server - align 2 sequences with all possible varieties of dynamic programming
• T-COFFEE - multiple sequence alignment
• ClustalW @ EBI - multiple sequence alignment
• MSA 2.1 - optimal multiple sequence alignment using the Carrillo-Lipman method
• BOXSHADE - pretty printing and shading of multiple alignments
• SIM4 - a program to align cDNA and genomic DNA
• Wise2 - align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools
• PipMaker - computes alignments of similar regions in two (long) DNA sequences
• VISTA - align + detect conserved regions in long genomic sequences