BioEdit: A FREE Sequence Alignment Editor

by on 20th of February, 2009 in Software & Online Tools
Avatar of Senthil Gandi
About Senthil Gandi
Gandi is a Ph.D student in Medical Microbiology at the University of Edinburgh. Having graduated with a degree in Biotechnology, merging cool scientific knowledge into industry became his interest. So he worked for two years for a small biotech company and realised doing a Ph.D was the way forward. He has a keen interest for new technologies and always thinking about spreading the great works of Bitesizebio further.

BioEdit is a biological sequence alignment editor supreme.

The author of this software calls it an intuitive multiple document interface with convenient features. What an understatement!

At the moment I only use a couple of functions of BioEdit. Mainly I use it to view chromatograms of sequencing results, to do sequence alignments, to reverse complement sequences, and to view amino acid compositions.

The list of functions available is just unbelievable, at the moment my usage only really scratches the surface of it’s capabilities.

The official BioEdit website lists the functions available on BioEdit. Here is just a snapshot of it’s capabilities:

  • Four modes of manual alignment: select and slide, dynamic grab and drag, gap insert and delete by mouse click, and on-screen typing which behaves like a text editor.
  • In-color alignment and editing with separate nucleic acid and amino acid color tables and full control over background colors.
  • Plasmid drawing interface for automated creation of plasmid vector graphic from a DNA sequence. Easily mark positions, add features with arrows and curved boxes, and mark restriction enzyme cut sites. Also show detail of polylinker and draw moveable arrows and shapes with drawing tools.
  • Dynamic information-based alignment shading.
  • Point-and-click color table editing
  • Display and print ABI chromatograms with professional-looking output.
  • Group sequences into groups or families.
  • Lock alignment of grouped sequences for synchronized hand alignment adjustments.
  • Annotate sequences with graphical features with dynamic view in alignment windows including feature annotation information tooltips.
  • Lock sequences to prevent accidental edits.
  • Specify characters to be considered valid for calculations in amino acid and nucleotide sequences.
  • Sort sequences by name, LOCUS, DEFINITION, ACCESSION, PID/NID, REFERENCES, COMMENTS or by residue frequency in a selected column.
  • Merge alignments through a reference sequence.
  • Append one alignment to the end of another.

If this impresses you, then the full list and the screenshots will blow your mind.

In addition, several sequence manipulation, analysis programs and links to external analysis programs are easily accessible from BioEdit. One of the external applications that I use alot is ClustalW… so that’s one less program I need to run on your computer.

Whether you do a little or a lot of Bioinformatics, I think it is a piece of software that you should definitely try.

The downsides of BioEdit?

Well one is that it only runs on Windows based computers, it is slightly memory demanding, and the author has stopped maintaining this program – although he does offer email-based support.

But nonetheless, as a user of BioEdit I have no complaints. For a freeware program it is simply one of the best pieces of bio-software out there.

If you are looking for more free software, take a look at our top 10 bio-related software for PC and Mac. Or, if you like to keep it in your browser, have a look at what the Molecular Biology toolbar has to offer.

If you have tried BioEdit, tell us your views on the program!

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