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.

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

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

FinchTV

This program will allow the user to view and extract sequence data from trace files. There is a Mac version of FinchTV.
Click here to download the FinchTV

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