Of these only JalView, like DNAAlignEditor, is open source. Mainly I use it to view chromatograms of sequencing results, to do sequence alignments, to reverse complement sequences, and to view amino acid compositions. If this happens, you may want to try Oh yeah, I almost forgot, the author of BioEdit is: Tom Hall Ibis Therapeutics A division of Isis Pharmaceuticals 1891 Rutherford Road Carlsbad, CA 92008 76 Heckles can be directed to. Guide to editing sequences with Chromas and BioEdit Guide to editing sequences with Chromas and BioEdit By Peter Unmack Editing chromatograms with Chromas Chromas has the advantage the you can save all of your chromatograms which can subsequently be used in any other programs unlike Sequencher which saves everything in a project file which cannot be opened by anything else. If I loose my sequence alignment, at least all my chromatograms with the correct edits are still there to rebuild it from. BioEdit can also edit chromatograms, but I find Chromas to be nicer. Double click on the chromatogram file usually has the extension ab1. This opens the file in Chromas see below under installation notes if some other program opens it instead of Chromas. The chromatograms come off the machine with all bases in upper case. I usually make all of my edits as lower case bases as it makes it easier to identify where I have made edits.

When I am done I save the chromatogram and export the data to a line file which is saved with a. Alternatively, you can go edit, copy sequence, FASTA format and paste that into BioEdit. One trick I find useful later is to always edit your sequences from the same starting base unless the starts are all messy, as it makes sequence alignment much easier later. Each of the commercial versions have a free 60 day trial should you wish to try them.

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