CAT: A Cross-species Alignment Tool
CAT is named after Cross-species Alignment Tool. It is designed to be a cross-species (both intra-species and inter-species), nucleotide level, cDNA-to-genome alignment software. It uses improved heuristics to effectively balance specificity, sensitivity and speed, and is optimized for genome-wide mapping.
Project details are here, with downloads and documentation.
An article describing CAT is freely available in BMC Bioinformatics.