ProSeq  is a Windows and Linux (no mac version, sorry) program for convenient chromatogram and sequence editing, multiple sequence alignment, assembly and checking of DNA polymorphisms datasets and basic population genetic (DNA polymorphisms, neutrality tests etc) and even more basic phylogenetic analyses.

The latest version 3 was specifically designed to handle multigenic datasets. E.g. it can do multiple alignment of many genes in one go. The analysis of DNA polymorphism for multiple genes can also be done with a single mouse click. It has been tested with up to 10000 genes.

To facilitate the work with multigenic datasets ProSeq3 allows one to create a relational database where sequences from different genes 'relate' to specific individuals. I.e. if multiple genes are sequenced from a set of individuals, it is possible to link each sequence to the specific individual it comes from.

Other new developments include quite useful and fairly flexible visual representation of the data, as shown below. It also allows to open and save data in many popular file formats, so the program is also handy for shuttling data between other programs.

The most recent developments include a number of Illumina & 454-related functions, such as data input in SAM and maq formats.

Free download:

The program is completely free. "Demo" note on this picture appeared when I used a demo tool to produce this animated gif file.