Cross_match is a general purpose application for comparing any two DNA sequence sets. For example, it can be used to compare a set of reads to a set of vector sequences and produce vector-masked versions of the reads, a set of cDNA sequences to a set of cosmids, contig sequences found by two alternative assembly procedures (for example, phrap and xbap) to each other, or phrap contigs to the final edited cosmid sequence. It is slower but more sensitive than BLAST.

Cross_match is required and/or recommended by some packages available on Bio-Linux such as trace2dbest.

Cross_match is licensed software and thus is not installed by default on Bio-Linux. It is free to academic researchers and comes as part of the phrap package, but you must obtain a license to get the software. Further information on how to obtain phrap/cross_match/swat is available on the official website for phred, phrap and consed.