I have tried most of the Solexa/illumina capable free short read aligners (e.g. Eland, MAQ, Novoalign, Shrimp, BWA, Bowtie, SOAP, Mosaik) and have had variable degrees of success/satisfaction with them. I generally flip-flop between MAQ and Novoalign but BWA may prove to replace MAQ in the near future. I am wondering if anyone who has bought into the commercial alignment software could share their stories. I'm interested to know if there are real benefits to forking over the money for a license to these programs (some examples are the Synamatix package or the commercial version of Novoalign). Anyone with positive or negative feedback on the commercial tools is welcome to post their comments here.