Tom Hall. North Carolina State University, Department of Microbiology. This is likely to be the final release of BioEdit. There may be some bugs. BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student. BioEdit can also edit chromatograms, but I find Chromas to be nicer. MEGA also has an alignment editor, but I’ve not really used it very much. Double click on the .

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I always keep the BioEdit file with all forwards, reverses and consensus sequences so that if I double check stuff later it is easier to find the relevant chromatograms I can tell what sequence is from where by the sequence name.

Sequence editing using BioEdit

I paste these into Microsoft Word and use search and replace to get rid of extra details. All of that probably sounds very tytorial, once you have carefully worked through it a couple of times it becomes very easy.

Be careful to copy. Select all the reverse sequences and cut them. There is no auto save function.

Sequence editing using BioEdit

It helps if you edit the sequences to start from the same base prior to importing them, that way if you do multiple sequences they are already mostly aligned. You can download my bioedit. Change the view type on the lower toolbar 3rd of the alignment windowselect the third colored button from the left says Shade identities and similarities when you hold the mouse over it. Then I run a NJ analysis to see what is going on with the dataset.


At the end of this phase you have done two data checks, one when you edited your original chromatogram, second when you checked any unique base pair changes.

Guide to editing sequences with Chromas and BioEdit

Adjust the size tutoria, the chromatogram trace with the Horizontal scale and Vertical scale bars to the top left of the image. Since this may interfere with analysis of the sequence, these will have to be edited out. I first group all the forwards together, then all the reverses.

Now place the cursor in the same place in the consensus sequence. I check any unique differences by opening the chromatogram. These should show an almost exact match to the forward or reverse sequence. Click on the view menu, and check editable bioefit. Select them all control-acopy to clipboard control-cgo back to BioEdit, to paste these names over the existing ones.

Note that I have changed or set many menu short cuts see BioEdit stuff to change after installation below to make things quicker, thus these instructions are based on these changes.

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. Hit save control-shift-s and repeat for each group of sequences.

I copy the sequence titles to the clipboard Edit, Copy sequence titles. Copy the data of highlighted sequence. Look in the Desktop or wherever else you saved the edited sequence filesfiles of tutprial All files.


Indication of selected region on the aligment window not changed. Each group should choose one of the sequence files on the disk, and copy it from drive A to the desktop. Select to the beginning including the current residue. To change settings first create a new alignment File, New Alignment or open gioedit existing file.

Guide to editing sequences with Chromas and BioEdit

Much editing in BioEdit requires extensive repetitive actions, so using the menus will rather slow. I use BioEdit to align sequences as it is free and has some handy features.

To correct the consensus sequence I copy and paste the sequences from a population or individual, group, etc. Note that sequences after bases become increasingly unreliable, and are not worth spending much time on. This highlights any columns that have different bases. Double click on the chromatogram file usually has the extension ab1. The sequence present in the original file is the sequence of the newly synthesized strand.

BioEdit lets you modify just about anything that it does relative to menus and keyboard short cuts as well as the default settings for displaying data. Click on File menu, Open.

If the program sticks the.