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    • Free Bioinformatics Software

     

    All in One Software Bundles

    Staden Package

    Staden is very large and powerful DNA assembly and analysis program. This software will run under many different operating systems, Unix, Linux, Windows and Mac. A large manual, tutorial files and other support can be found at the web site. Installation files may be obtained at the Staden download site on Sourceforge For more information on Staden and installing it for Windows XP, Vista, or 7, please click here. It was last updated in July, 2019.

    GeneStudio

    Genestudio is former commercial software, now available free-of-charge. It allows DNA manipulation, trace sequence assembly, tree drawing and also contains a file converting utility called SeqVerter. I use Contig, the trace assembly program now, instead of DNAStar's SeqMan. DNAStar raised the price of a sequence editor, primer-select and SeqMan package to $599 per year! No longer affordable and this free program does everything I need to assemble Sanger trace files Download GeneStudio here.

     

    BLAST (Basic Local Alignment Search Tool)

    If you have a sequence of DNA or protein and want to know more about you can search GenBank for similar (oridentical) sequences using BLAST.

    Click here for the BLAST page.

    BioEdit

    This program was written to align DNA then it just grew and grew. It has incorporated at least a dozen other DNA software programs. It's great strength is that is it can use and export many different file formats. It is Freeware. This suite of programs is no longer supported but has been updated in 2013. Some of the programs may not run under Windows 7. It’s still a very useful collection of programs if you are running Windows XP or if you have virtual XP under Windows 7. Click here to download the program For more information on BioEdit and installing it for Windows XP, Vista, or 7, please click here.

     

    Trace File Viewers

    Chromaseq

    This is a free DNA sequence program that runs within Mesquite, a phylogeny program. You need to get the programs Phred and Phrap (see the Fred Green lab on the Useful Links page). It is a very powerful program.
    Click here for the web site.

    SnapGene Viewer

    SnapGene Icon

    This is a free version of commercial software. It will display trace files but even the free version will do a lot more, such as DNA editing, Blast searches, etc. There are Windows and Mac versions.
    Click here to download SnapGene

    SeqTrace

    SeqTrace icon

    This is a fully operational trace assembly and viewer program. It will only work with those trace files containing weights. So files from newer projects. There are Windows, Mac and Linux Versions
    Click here to download SeqTrace

    Chromas Lite

    This program will allow the user to view and extract sequence data from trace files.

    Click here to download the Chromas Lite

    Trace File Viewers are also available in Staden and BioEdit

     

    DNA Manipulation Programs

    pDraw

    This is a really nice, simple Freeware (Beerware) program. It’s main use is to easily draw plasmid constructs for slides, posters or other presentations. You can also construct restriction maps and run mock agarose gels. Click here for more information and to download It is updated frequently and some questions may be answered in the forums.

     

    Alignment Programs

    CLUSTAL

    CLUSTAL  is a program for aligning multiple nucleic acid or protein sequences. There are several versions of CLUSTAL and many DNA software programs incorporate one or another.  ClustalX is a stand alone version. When it is installed on your computer you can align sequences without connecting to the internet. Click here to download a version of Clustal and view updates

    MEGA

    MEGA is alignment and phylogeny software. It allows you to align DNA or protein sequences and infer evolutionary relationships. It is well supported and works on many platforms, Windows, Mac, Unix, etc. There is a textbook, Molecular Evolution and Phylogeny that provides a great deal of theory behind the comparison process. The MEGA web site provides a lot of information and support and is the source of the program. There are some very useful tutorials as well.

    MAUVE

    MAUVE is multiple alignment of conserved genomic sequence with rearrangements. This free program from the University of Wisconsin-Madison allows genome alignment on a desktop computer and works under Windows, MAC and Linux operating systems. Click here to download MAUVE

     

    Phylogeny Programs

    MEGA

    MEGA is alignment and phylogeny software. It allows you to align DNA or protein sequences and infer evolutionary relationships. It is well supported and works on many platforms, Windows, Mac, Unix, etc. There is a textbook, Molecular Evolution and Phylogeny that provides a great deal of theory behind the comparison process. The MEGA web site provides a lot of information and support and is the source of the program. There are some very useful tutorials as well.


    Utilities

    SeqVerter

    This is a free stand-alone program from Genestudio, a commercial molecular biology software company. It is a very useful file converter program. It can be downloaded at GeneStudio

     

     

     

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