||BioEdit is a mouse-driven, easy-to-use sequence
alignment editor and sequence analysis program designed and written by
a graduate student who knows how frustrating and time consuming it can
be to rely upon word-processors and command-line programs for sequence
manipulation. BioEdit is intended to supply a single program that can handle
most simple sequence and alignment editing and manipulation functions that
researchers are likely to do on a daily basis, as well as a few basic sequences
BioEdit offers a variety of useful features:
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
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.
Rudimentary phylogenetic tree viewer (for phylip-format
trees) that allows node flipping and printing.
Verbally read back sequences in single sequence editor
to verify hand-typed sequence entries.
Reads and writes Genbank, Fasta, Phylip 3.2, Phylip
4, and NBRF/PIR formats. Now also reads GCG and Clustal formats
Utilizes Don Gilbert's ReadSeq to automatically import
and export 11 additional formats, including MSF, ASN.1, IG/Stanford and
Allows import of compatible formats directly from
the clipboard without saving to a file first.
Easy customization of menu shortcuts for editor window
RNA comparative analysis, including covariation,
potential pairings and mutual information analysis (currently capable of
generating matrices up to 10,000 x 10,000 -- but this would be a 600+ Mb
file) with matrix plotter for 2-D matrix output tables and area graphing
for individual rows of a data matrix. Matrix plotter and line graphs
both have point-and-click data selection and the matrix plotter and 1-D
line graphs of matrix data are now dynamically linked
View sections of very large matrices with plotter
(tested on up to a 5183 x 5183 matrix = 180 Mb file)
View and manipulate alignments up to 20,000 sequences.
Binary file format (BioEdit Project format) for fast
open and save of large alignments -- the 6205 sequences of the prokaryotic
16S rRNA alignment (29 Mb file) open and save in less than 10 sec on a
233 MHz Pentium.
ORF searching with user-defined preferences
Formatted translations of nucleic acid sequences
with codon usage summary, choice of one- or three-letter amino acid
codes, translation of selected region only of nucleic acid, and choice
of start/stop codons
Split window view for simultaneous and synchronized
editing of two different places in the same file -- split window vertically
Amino acid and nucleotide composition analyses and
Align protein-encoding nucleic acid sequences through
amino acid translation.
ClustalW multiple sequence alignment (interface internal,
external program by Des Higgins et. al.) with auto-update of aligned protein
full titles and GenBank field information, as well as nucleotide coding
sequence when aligned from a protein view of nucleotide sequences.
Protein hydrophobicity/hydrophilicity plots
Protein hydrophobic moment matrix plots (0-180 dgrees)
Full choice of system fonts now available in edit
Restriction mapping with any or all-frame translation,
multiple enzyme choice and output options, and circular DNA capability
Browse restriction enzymes by manufacturer
Sequences at least 4.6 Mb in length can be manipulated
(the largest sequence tested so far is the E. coli genome (4.6 Mb)
-- E. coli was opened, reverse complemented, translated into 10,125 codon
stretches >=100 amino acids, and opened and saved with full GenBank annotation).
Six-frame translations capable of raw translation
of entire genomes (tested with the E. coli genome -- ca. 4.6 Mb)
Save GenBank format Entrez files with LOCUS, DEFINITION,
ACCESSION, PID, NID, DBSOURCE, KEYWORDS, SOURCE, REFERENCE, COMMENT, and
FEATURES fields intact. Modify or add your own information. Multiple sequence
files saved in GenBank format retain any entered information.
This information is also saved in the BioEdit Project file format.
Configure and run accessory applications via
the BioEdit graphical application configuration interface. BioEdit currently
(install package -- install separately)
Phylip programs including:
Full NCBI package of local BLAST programs, database
creation, and internet BLAST client 2.0, with sample protein database of
coli open reading frames.
Shaded graphical output with identity and similarity
(for protein) shading and several formatting options.
Rich text export of formatted, shaded alignments
On-line help system (always a couple of versions
behind the program).
Entropy (information lack) plotting.
Multiple document interface.
Basic sequence manipulations (reverse/complement,
Easy text export and configurable text printing.
PC-compatible i486+ computer running
Windows 95, 98, NT or 2000. A pentium with at least 32 Mb of RAM is recommended.
About 30 - 40 Mb of free disk space are also required (BioEdit install
will take 15 Mbytes, but the temporary directory requires ca. 15 Mb and
the BioEdit.zip file takes 8 Mb).
Download the file BioEdt.zip.
Unzip it to a temporary directory, then run "setup.exe". Follow the on-screen
instructions and BioEdit will install itself.
BioEdit comes at the high cost of $0.00.
It also comes with a triple-your-money back guarantee. The nature of this
guarantee is this:
If you're not 100% satisfied with BioEdit
or any aspect of your life, I'll refund triple the above listed price of
BioEdit (nothing). This guarantee also comes with the following disclaimer:
DISCLAIMER: NO (real) GUARANTEE, EXPRESSED OR
IMPLIED, IS MADE AS TO THE SUITABILITY OF THIS SOFTWARE FOR ANY PURPOSE
NOR FOR ANY COMPUTER OR PERSON. YADDA, YADDA, YADDA, AND THE AUTHOR SHALL
NOT BE HELD RESPONSIBLE, NOR BE LIABLE FOR IN ANY WAY, ANY DAMAGE OCCURING
TO EQUIPMENT OR HEALTH WHILE USING THIS SOFTWARE.
BioEdit.zip (Full install: ca. 11.9 Mb)
Note: There is an occasional problem with transmission of the
BioEdit.zip file (some people have gotten CRC errors when unzipping the
If this happens, you may want to try downloading
the installation in smaller chunks (click here to go to download page).