A series of pictures of different lab equipment associated with DNA processing.

Analysis Software

GeneMapper Software for fragment analysis. This replaces GeneScan/Genotyper. We provide two stand alone Dell PC workstations both equipped with the latest version of Genemapper, free for our customers located on site at 21 Sachem Street, Office Room 148, New Haven, Ct.

GeneMarker This software has been designed and created in order to provide genetic researchers with a biologist friendly genotyping analysis tool, it is much less expensive than GeneMapper.

STRand It is very convenient and easy to use. The set-up is not intuitive, but their support staff is very helpful.

Peak Scanner A new easy to use software tool from Applied Biosystems is available as a free download. This software allows users to view, edit, analyze, print and export fragment analysis data from files generated by Applied Biosystems instruments.

Formatting and File conversion Software

Gm Convert For everybody who uses GeneMapper, this piece of software should make life easier (as far as data formatting is concerned anyway). This is an executable (os x, windows) and Python command line (all platforms) program to re-array data output by GeneMapper (AppliedBiosystems).

Formatomatic Population Genetic File Creator and Converter, this program adds quite a few formatting options to other available toolkits.

3730 Conversion Utility For modifying 3730 files to work with Genescan, click the link to download the program.

Repeat Search, Primer Design and PCR utilities

MsatCommander msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatfinder will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).

BioPHP microsatellite repeat finder

Perfect Microsatellite Repeat Finder- open source application will help locate microsatellite repeats.
Primer3Plus pick primers from a DNA sequence
PerlPrimer open-source PCR primer design

Data Transformation and Analysis Software

Data Transformation and Preliminary Analysis:
Msat
MsatToolkit
Genalex

Multi-Purpose:
Arlequin
Genepop (web version) or Genepop

Specialized:
Assignment and Hybridization
Structure
NewHybrids

Landscape Genetics
R: http://lib.stat.cmu.edu/R/CRAN/
R Geneland package (installation within R) instructions

Relatedness
Cervus
Kingroup

Multi-Purpose ‘Borrowed’ Software:

PAST is a free, easy-to-use data analysis package originally aimed at paleontology but now also popular in ecology and other fields. Inspired by PALSTAT, it includes common statistical, plotting and modeling functions