Developer: Tom Hall
- How To Use Bioedit Software
- Bioedit Software Free For Macbook Pro
- Bioedit Software Free For Mac Download
Supported platforms: Windows 95 and higher
To my knowledge, BioEdit is the most comprehensive biological sequence alignment editor. Most of my labmates run this software using Parallels Desktop. For some of them, BioEdit is the only reason to install Parallels Desktop. I need to edit my alignment recently, and install it in my iMac using Wine, which is a compatibility layer for running Windows applications on POSIX-compliant OS.
Download: http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Features
View Quality scores
No
- Vector NTI; Vector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 (Panther).Features create, annotate, analyse, and share DNA/protein sequences perform and save BLAST searches design primers for PCR, cloning, sequencing or hybridisation experiments plan cloning and run gels in silico align.
- BioEdit is a software program that embeds the tools that scientists and technicians need so they perform specific tasks, such as manipulation of sequence alignment, ABI tracing or RNA analysis. The program's GUI is severely outdated, mostly because it was designed to operate in older OS, like Windows95/98/NT.
View raw data
Yes
Assembly
Yes, but you have to manually align up each sequence and manually create a consensus sequence (which other programs are very good at).
Input file formats
ABI files (.abi and .ab1), FASTA, Genbank, Fasta, Phylip 3.2, Phylip 4, GCG, Clustal, and NBRF/PIR formats (a complete list can be found in the manual).
Output file formats
ABI files, text files, FASTA, Genbank, Fasta, Phylip 3.2, Phylip 4, GCG, Clustal, and NBRF/PIR formats (a complete list can be found in the manual).
Trimming
No trimming of low quality regions
Integrated Blast
Yes
Open multiple windows
Yes
Edit bases
Yes
ABI limits (regions outside of clear range region are displayed in grey)
Earth stove 3340 manual. No
Other functions
- Reverse complement sequence
- Rudimentary phylogenetic tree viewer
- Plasmid drawing and restriction site mapping
- Translation
- ClustalW multiple sequence alignment
A complete list can be found on the BioEdit website
Cost
Free, but no longer maintained. The website seems to also be down these days. We have a copy of the installer if anyone wants to get a copy.
How To Use Bioedit Software
Comments
BioEdit is free and provides many basic functions for protein and nucleic sequence editing, alignment, manipulation and analysis. The software can still be downloaded but it is no longer maintained. If you only need a trace viewer or want to do basic editing other free software options are better because they have more trimming options and display the quality values (phred scores). However, if you are looking for a free alignment program BioEdit might be right for you.
This page is a subsection of the list of sequence alignment software.
Multiple alignment visualization tools typically serve four purposes:
- Aid general understanding of large-scale DNA or protein alignments
- Visualize alignments for figures and publication
- Manually edit and curate automatically generated alignments
- Analysis in depth
The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is necessary because algorithms for both multiple sequence alignment and structural alignment use heuristics which do not always perform perfectly. The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
Alignment viewers, editors[edit]
Bioedit Software Free For Macbook Pro
Name | Structure prediction tools integrated | Can align sequences | Can calculate phylogenetic trees | Other features | Format support | License | Can run on Browser | Operating Platforms | Link |
---|---|---|---|---|---|---|---|---|---|
Alan | No | No | No | Allows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwarding | FASTA, Clustal | Free, GPL 3 | No | Linux Terminal | Official website |
Ale (emacs plugin) | No | Yes | No | No | GenBank, EMBL, FASTA, PHYLIP | Free, GPL | No | GNU Emacs | Official website |
AliView 2019 | No | MUSCLE integrated; other programs such as MAFFT can be defined | External programs such as FastTree can be called from within | Fast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design. | FASTA, FASTQ, PHYLIP, Nexus, MSF, Clustal | Free, GPL 3 | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
alv | No | No | No | Console-based (no GUI), yet with colors. Coding DNA is coloured by codon. | FASTA, PHYLIP, Nexus, Clustal, Stockholm | Free, GPL 3 | No | Cross-platform | Official website, see also alv on GitHub |
arb | structure editable, show bond in helix sequence regions, 2D molecule viewer | MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference) | arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayes | Edits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and visualizes probes. | FASTA, GenBank, EMBL, Newick | Proprietary, freeware, arb license, open modifiable source | No | Linux, Mac OS (homebrew) | Official website |
Base-By-Base | No | MUSCLE | UPGMA, NJ, complete and single linkages, WPMGA | Visual summary, percent identity tables, some integrated advanced analysis tools | Genbank, FASTA, EMBEL, Clustal, base-by-base files | Proprietary, freeware, must register | ? | ? | Official website |
BioEdit | No | ClustalW | Rudimentary, can read PHYLIP | Plasmid drawing, ABI chromatograms, | Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIR | Proprietary, freeware | No | Windows (95/98/NT/2000/XP) | Official website |
BioNumerics | No | Yes | Yes | ? | Genbank, FASTA | Proprietary, commercial | ? | ? | Official website |
bioSyntax | No | No | No | Native syntax highlighting support for Vim, less, gedit and Sublime | FASTA, FASTQ, Clustal, SAM, VCF and more | Free, GPL 3 | No | Vim, Less, GEdit, & Sublime | Official website |
BoxShade | No | No | No | Specifically for multiple alignments | MSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalW | Free, public domain | No | MSDOS, VMS | Official website |
CINEMA | No, but can read-show 2D structure annotations | ClustalW | No | Dotplot, 6 frame translation, Blast | Nexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTS | Proprietary, freeware | No | Cross-platform -Mac OS, Linux, Windows | Official website |
CLC viewer (free version) | Commercial version only | Clustal, MUSCLE, T-Coffee, MAFFT, Kalign, various | UPGMA, NJ | Workflows, blast-genbank search | many | Proprietary, freeware. More options available in commercial versions. | No | ? | Official website |
ClustalX viewer | No | ClustalW | NJ | Alignment quality analysis | Nexus, MSF, Clustal, FASTA, PHYLIP | Proprietary, freeware for academic use | No | Command line | Official website |
Cylindrical Alignment App | No | No | No | 3D, animation, drilldown, legend selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | Free, CDDL 1. Available for dual licensing. | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
Cylindrical BLAST Viewer | No | No | No | 3D, animation, drilldown, legend selection | BLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLT | Free, GPL | ? | ? | Official website |
DECIPHER | Yes | Yes | UPGMA, NJ, ML | Primer-Probe design, Chimera finding | FASTA, FASTQ, GenBank | Free, GPL | No | Mac OS, Windows | Official website |
Discovery Studio | Yes | Align123, ClustalW, S-ALIGN | UPGMA, NJ, with bootstrap and best tree | Visualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, more | BSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, .. | Proprietary, commercial, Viewer is Freeware | ? | Linux, Windows | Official website |
DnaSP | ? | ? | ? | Can compute several population genetics statistics, reconstruct haplotypes with PHASE | FASTA, Nexus, MEGA, PHYLIP | Proprietary, commercial, freeware for noncomercial use | ? | Cross-platform -Mac OS, Linux, Windows | Official website |
DNASTAR Lasergene Molecular Biology Suite | Yes | Yes | Yes | Align DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translation | ABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, Phred | Proprietary, commercial, academic licenses available | ? | Mac OS, Windows | Official website |
emacs - biomode | ? | ? | ? | ? | ? | Free, GPL | ? | ? | Official website |
FLAK | No | Can perform fuzzy whole genome alignment | No | Very fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy options | FASTA | Proprietary, commercial, freeware for noncommercial use | ? | ? | Official website |
Genedoc | No, but can read-show annotations | Pairwise | No, but can read-show annotations | gel simulation, stats, multiple views, simple | many | Proprietary, freeware | ? | ? | Official websitetable of features |
Geneious | Yes - powered by EMBOSS tools | Clustal, MUSCLE, MAUVE, profile, translation | UPGMA, NJ, PhyML, MrBayes plugin, PAUP* plugin | Whole genome assembly, restriction analysis, cloning, primer design, dotplot, much more | >40 file formats imported and exported | Proprietary, commercial; personal, floating | ? | Cross-platform - Mac, Windows, Linux | Official website |
Integrated Genome Browser (IGB) | No | No | No | Sequences and features from files, URLs, and arbitrary DAS and QuickLoad servers | BAM, FASTA, PSL | Free, CPL | ? | Cross-platform - Mac, Windows, Linux | Official website |
interactive Tree Of Life (iTOL) | No | No | ? | Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments. | FASTA | Proprietary, free use | Yes | Browser | Official website |
IVisTMSA | No | Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment | Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx | Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator | ClustalW, MSF, PHYLIP, PIR, GDE, Nexus | Proprietary, freeware | ? | ? | www.ivistmsa.com |
Jalview | Secondary structure prediction via JNET | Clustal, MUSCLE, MAFFT, Probcons, TCoffee via web services | UPGMA, NJ | Sequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval. | FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm | Free, GPL | Applet | Cross-platform -Mac OS, Linux, Windows | Official website |
Jevtrace | Integrated with structure viewer WebMol | No | No | A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. | FASTA, MSF, Clustal, PHYLIP, Newick, PDB | Proprietary, commercial, freeware for academic use | ? | Cross-platform -Mac OS, Linux, Windows | Official websitemanual |
JSAV | No | No | No | A JavaScript component allowing integrating an alignment viewer into web pages | An array of JavaScript objects | Free, GPL 2 | Yes | Browser | Official website |
Maestro | Yes | ClustalX | Yes | Mapping from sequence to 3D structure, structure-sequence editing-modeling | Clustal, FASTAPDB | Proprietary, freeware for academic use | ? | ? | Official website |
MEGA | No | Native ClustalW | UPGMA, NJ, ME, MP, with bootstrap and confidence test | Extended support to phylogenetics analysis | FASTA, Clustal, Nexus, MEGA, etc. | Proprietary, freeware, must register | ? | ? | Official website |
Molecular Operating Environment (MOE) | Yes | Yes | Yes | Part of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc. | Clustal, FASTA, PDB, EMBL, GCG, GCG_MSF, Genbank, PHYLIP, PIR, raw_seq | Proprietary | ? | ? | Official website |
MSAReveal.org | No | No | No | Optional coloring. Touching AA shows 3-letter code and sequence number. Touching consensus shows AA frequencies in that column. Counts and percentages of aromatics, charged, gaps. | FASTA | Free, Creative Commons Attribution NonCommercial Share-alike | ? | ? | Official website |
Multiseq (VMD plugin) | No, but can display and align 3D structures | ClustalW, MAFFT, Stamp (Structural) | Percent identity, Clustal, MAFFT, Structural | Scripting via Tcl, mapping from sequence to 3D structure | FASTA, PDB, ALN, PHYLIP, NEXUS | Proprietary, freeware, but VMD is free for noncommercial use only | ? | ? | Official website |
MView | No | No | No | Stacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patterns | BLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSF | Free, GPL | No | Cross-platform - Mac OS, Linux, Windows | Official website |
PFAAT | No, but can display 3D structures | ClustalW | NJ | Manual annotation, conservation scores | Nexus, MSF, Clustal, FASTA, PFAAT | Proprietary, freeware | ? | ? | Official website |
Ralee (emacs plugin for RNA al. editing) | ? | RNA structure | ? | ? | Stockholm | Free, GPL | ? | ? | Official website |
S2S RNA editor | 2D structure | Rnalign | No | Base-base interactions, 2D-3D viewer | FASTA, RnaML | Proprietary, freeware | ? | ? | Official website |
Seaview | No | local MUSCLE-ClustalW | Parsimony, distance methods, PhyML | Dot-plot, vim-like editing keys | Nexus, MSF, Clustal, FASTA, PHYLIP, MASE | Proprietary, freeware | ? | ? | Official website |
Seqotron | No | MUSCLE, MAFFT | UPGMA, NJ, ML (Physher) | Manual alignment, tree visualisation | Nexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flat | Free, GPL | ? | Mac OS X | Official websitepublication |
Sequilab | Yes | Yes | No | Link alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbars | Accession number, GI number, PDB ID, FASTA, drag-drop from external URL from within the user interface | Proprietary, freeware | ? | ? | Official website |
SeqPup | No | ? | ? | ? | ? | Proprietary, freeware | ? | ? | Official website |
Sequlator | No | Pairwise alignment | No | easy alignment editing | MSF | Proprietary, freeware | ? | ? | Official website |
SnipViz | No | No | No (but can display them) | Pure Javascript and HTML; suitable to integrate in websites | FASTA, newick | Free, Apache 2.0 | Yes | Browsers | Official website, publication |
Strap | Jnet, NNPREDICT, Coiled coil, 16 different TM-helix | 15 different methods | NJ | Dot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, BioJava-interface | MSF, Stockholm, ClustalW, Nexus, FASTA, PDB, Embl, GenBank, hssp, Pfam | Free, GPL | ? | ? | Official website |
Tablet | No | No | No | High-performance graphical viewer for viewing next generation sequence assemblies and alignments. | ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3 | Free, BSD 2-clause | ? | ? | Official website |
UGENE | Yes | MUSCLE, Kalign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith–Waterman algorithm | Yes | Many | FASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFF | Free, GPL | ? | ? | Official website |
VISSA sequence-structure viewer | DSSP secondary structure | ClustalX | No | Mapping from sequence to 3D structure | Clustal, FASTA | Proprietary, freeware | ? | ? | Official website |
DNApy | No | MUSCLE | No | Editing of GenBank files, plasmid drawing, ABI chromatograms, | FASTA, FASTQ, GenBank | Free, GPL 3 | ? | ? | Official website |
Alignment Annotator | Yes | By sequence or mixed sequence and structure | Includes Archaeopteryx | DAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview. | Many | Free, GPL | Yes | iOS, Android, MS-Mobile, Browsers | Official website |
See also[edit]
Bioedit Software Free For Mac Download
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