BioEdit - Sequence Alignment Editor and Sequence Analysis Software Program

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 analyses. 

BioEdit offers a variety of useful features:

1. 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.
2. In-color alignment and editing with separate nucleic acid and amino acid color tables and full control over background colors.
3. 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.
4. Dynamic information-based alignment shading.
5. Point-and-click color table editing
6. Display and print ABI chromatograms with professional-looking output.
7. Group sequences into groups or families.
8. Lock alignment of grouped sequences for synchronized hand alignment adjustments.
9. Annotate sequences with graphical features with dynamic view in alignment windows including feature annotation information tooltips.
10. Lock sequences to prevent accidental edits.
11. Specify characters to be considered valid for calculations in amino acid and nucleotide sequences.
12. Sort sequences by name, LOCUS, DEFINITION, ACCESSION, PID/NID, REFERENCES, COMMENTS or by residue frequency in a selected column. 
13. Merge alignments through a reference sequence.
14. Append one alignment to the end of another.
15. Rudimentary phylogenetic tree viewer (for phylip-format trees) that allows node flipping and printing.
16. Verbally read back sequences in single sequence editor to verify hand-typed sequence entries.
17. Reads and writes Genbank, Fasta, Phylip 3.2, Phylip 4, and NBRF/PIR formats.  Now also reads GCG and Clustal formats
18. Utilizes Don Gilbert's ReadSeq to automatically import and export 11 additional formats, including MSF, ASN.1, IG/Stanford and EMBL.
19. Allows import of compatible formats directly from the clipboard without saving to a file first.
20. Easy customization of menu shortcuts for editor window
21. 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
22. View sections of very large matrices with plotter (tested on up to a 5183 x 5183 matrix = 180 Mb file)
23. View and manipulate alignments up to 20,000 sequences. 
24. 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.
25. ORF searching with user-defined preferences
26. 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 
27. Split window view for simultaneous and synchronized editing of two different places in the same file -- split window vertically or horizontally
28. Amino acid and nucleotide composition analyses and plots
29. Align protein-encoding nucleic acid sequences through amino acid translation.
30. 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. 
31. Protein hydrophobicity/hydrophilicity plots
32. Protein hydrophobic moment matrix plots (0-180 dgrees)
33. Full choice of system fonts now available in edit window
34. Restriction mapping with any or all-frame translation, multiple enzyme choice and output options, and circular DNA capability
35. Browse restriction enzymes by manufacturer
36. 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).
37. Six-frame translations capable of raw translation of entire genomes (tested with the E. coli genome -- ca. 4.6 Mb)
38. 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.
39. Configure and run  accessory applications via the BioEdit graphical application configuration interface.
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41. Full NCBI package of local BLAST programs, database creation, and internet BLAST client 2.0, with sample protein database of E. coli open reading frames.
42. Shaded graphical output with identity and similarity (for protein) shading and several formatting options.
43. Rich text export of formatted, shaded alignments
44. On-line help system (always a couple of versions behind the program).
45. Entropy (information lack) plotting.
46. Multiple document interface.
47. Basic sequence manipulations (reverse/complement, translate, DNA->RNA->DNA)
48. Easy text export and configurable text printing.