| Our intent in the tutorial is to make the reader familiar with common file formats and with
general principles of genomic alignment programs. Both because of space limitations and for
clarity, only
the UCSC genome browser, the Spidey cDNA alignment tool, and the VISTA and PipMaker
genomic comparison tools are described in detail; however, we use many different
programs, web-based and locally installed, free and commercial, to create and
work with aligned sequences. In addition, new programs are constantly being published
and marketed. Below, we have listed some of the, mostly web-based, software
that we use. |