BioX
BioX 1.1b1
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(1) 2.5

Sequence analysis for biologists.   Free
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  • BioX has been discontinued
  • Developer
    Erik Lagercrantz
The goal of BioX is to bring easy-to-use sequence analysis to Mac-using biologists. It features graphical editors for sequences and multiple alignments, and supports opening and saving of many different sequence file formats. Analysis functions currently include searching for primers, restriction sites and repeats, calculating DNA melting temperature, translation and back translation, multiple alignment and more. Please note that this is a beta release.

BioX takes advantage of the Unix underpinnings of Mac OS X by using command line sequence analysis tools from the eBiotools package (which
What's New
Version 1.1b1:
  • [New] BioX is now a Universal Binary.
  • [New] Can create all-against-all dot plots showing similarity between sequences.
  • [New] Better overview when searching for restriction sites.
  • [New] Pattern search in sequences.
  • [New] Shows possible feature names in feature table editor.
  • [New] Includes Read Me, Release Notes, FAQ and home page links in Help menu.
  • [Changed] Changed menu shortcuts and titles for better consistency.
  • [Changed] Double click sequence name in an alignment to open the sequence for editing.
  • [Changed] Selecting in an alignment also marks the sequence names.
  • [Changed] Removed EMBOSS Launcher from the Tools menu.
  • [Changed] Dropped support for Mac OS X 10.3 Panther.
  • [Fixed] The last character in the file was ignored when reading fasta.
  • [Fixed] The application could crash when drawing restriction sites.
  • [Fixed] Error when dragging part of a sequence past the "end" of an alignment.
  • [Fixed] Some other minor bugs.
Version 1.1b1:
  • [New] BioX is now a Universal Binary.
  • [New] Can create all-against-all dot plots showing similarity between sequences.
  • [New] Better overview when searching for restriction sites.
  • [New] Pattern search in sequences.
  • [New] Shows possible feature names in feature table editor.
  • [New] Includes Read Me, Release Notes, FAQ and home page links in Help more...
Requirements
Intel/PPC, Mac OS X 10.3 or later, eBiotools installed, also free. (171 MB download)

*Previously available here








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BioX User Discussion (Write a Review)
ver. 1.x:
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+15

umijin reviewed on 07 Feb 2006
BioX is one of several recent Mac front ends for command-line interface applications used by molecular biologists. This software is still in BETA form, and it's apparent that there is still much to work out.

There is no actual documentation for BioX (that I can find), but there is a small article with general desriptions of function available on the developer website. Unfortunately, there are very few details.

In order to use BioX you must also obtain the EBioTools package. This is a 200MB download, and will install a package of comparable size. Although the above article claimed an install of 135MB, on my G4 Powerbook, it seems to have taken substantially more space -perhaps 500MB. It is also difficult to locate what is installed with EBioTools - I can't locate the directory these files are supposed to be intstalled in. So if hard drive space is a concern for you - don't download this package.

Opening BioX gives you a blank window, and it's easy to open and import molecular sequence files. The sequence and alignment viewer is nice, and you can easily edit/remove/insert sequences. BioZ will also do sequence alignments via the ClustalX package (included with EBioTools). This version of ClustalX appears to work much better than the latest stand alone versions I've used- though it's not clear what is different.

Unfortunately, there isn't much else you can do with the menu driven options for BioX. The 'sequence' menu has many useful options listed (e.g., complement, translation, search), but none of them are functional on my installation. It's not clear if these are features to be added, or BioX isn't working properly. There also is no help file.

The Emboss and Stad apps intalled with EBioTools are apparently accessible via the Tools menu. However, if you don't like command line interfaces, and the X11 window that pops up - this is not for you. It's not clear to me how to access other apps installed with EBioTools (e.g. Phylip), but perhaps again this is an intallatino issue.

So, BioX has some promise, but the size if the EBioTools install and the lack of any features other than alignment (which it seems to do well) makes it hard to recommend to others at this time.
[Version 1.0b2]


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Downloads:3,244
Version Downloads:2,695
Type:Education : Science
License:Free
Date:09 Sep 2006
Platform:PPC 32 / Intel 32 / OS X
Price:Free0.00
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The goal of BioX is to bring easy-to-use sequence analysis to Mac-using biologists. It features graphical editors for sequences and multiple alignments, and supports opening and saving of many different sequence file formats. Analysis functions currently include searching for primers, restriction sites and repeats, calculating DNA melting temperature, translation and back translation, multiple alignment and more. Please note that this is a beta release.

BioX takes advantage of the Unix underpinnings of Mac OS X by using command line sequence analysis tools from the eBiotools package (which contains software from the EMBOSS project, among others). By presenting these Unix tools in the form of a Mac application, BioX leverages the best of both worlds.

Some additional information and screenshots of BioX is available in the latest issue of EMBnet.news (Issue 2005:3, download PDF).


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