Sim4

Sim4 is a nucleotide sequence alignment program akin to BLAST but specifically tailored to DNA to cDNA/EST (Expressed Sequence Tag) alignment (as opposed to DNA–DNA or protein–protein alignment).  It was written by Florea et al. 

External links
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
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Category:Bioinformatics software
Category:Computational phylogenetics