Programs developed by Tom Hall
BioLign is a multiple contig alignment editor which constructs multiple alignments from the output generated. It allows integrated and synchronized viewing and unrestricted editing of both the base calls of the contig and the alignment itself. This is a great tool for alignment, SNP identification, and PHRAP evaluation.
An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer. Several sequence manipulation and analysis options and links to external analysis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations.