Aside from that limitation (which isn’t as bad as it might sound once you learn a few tricks), I really like its features. The most annoying aspect is that you have to manually align up each sequence and manually create a consensus sequence (which commercial programs like Sequencher and Geneious are very good at). I use BioEdit to align sequences as it is free and has some handy features. Each of the commercial versions have a free 60 day trial should you wish to try them. I’ve always used the free Chromas version, Chromas Lite, but there are two other versions with more features that are fairly cheap. 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. Alternatively, you can go edit, copy sequence, FASTA format and paste that into BioEdit. When I am done I save the chromatogram and export the data to a line file (which is saved with a. I usually make all of my edits as lower case bases as it makes it easier to identify where I have made edits. The chromatograms come off the machine with all bases in upper case. This opens the file in Chromas (see below under installation notes if some other program opens it instead of Chromas).

MEGA also has an alignment editor, but I’ve not really used it very much.ĭouble click on the chromatogram file (usually has the extension ab1). BioEdit can also edit chromatograms, but I find Chromas to be nicer. If I loose my sequence alignment, at least all my chromatograms with the correct edits are still there to rebuild it from. Guide to editing sequences with Chromas and BioEdit Guide to editing sequences with Chromas and BioEditīy Peter Unmack Editing chromatograms with ChromasĬhromas 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.

Bioedit align sequencing results