BioLign is a multiple contig alignment editor which constructs multiple alignments from the output generated by the PHRAP contig program (Phil Green, U. of Washington), and allows integrated and synchronized viewing and unrestricted editing of both the base calls of the contig and the alignment itself. Raw trace data is maintained and manual alignment adjustments as well as manual character insertions and deletions are synchronized automatically with the raw data. Sequence traces may visually inspected and edited in a synchronized interface which opens and closes traces automatically as you pass through them in the contig, and lines up all relevant traces at a user-defined point to the same point in the contig. A user-defined coloring scheme allows up to ten levels of coloring within the alignment window and the trace data view to reflect Phrap-assigned sequence quality. Traces graphically display Phred-assigned quality for each individual trace. BioLign was built upon the BioEdit interface (by the same author), and includes the entire BioEdit freeware package integrated with it. The alignment interface of a BioLign contig alignment is very similar to a BioEdit alignment document.
Tom Hall (THall@isisph.com)
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