The SCA (sequence composition analysis) takes a set of sequences in fasta format and generates a 2-dimensional crossed graph displaying the value of a given formula on the x-axis against the year of the sequences on the y-axis. The year is taken from the header line of each source sequence (starting with “>”). Additionally the points may be colored depending of the host the sequence is taken from.
CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.
SITES is a computer program for the analysis of comparative DNA sequence data. Basic analyses include: data summaries by polymorphism class; polymorphism estimates within and between groups (species); estimates of migration, neutral model, and recombination parameters; and linkage disequilibrium analyses. SITES is primarily intended for data sets with multiple closely related sequences. It is especially useful when multiple sequences have been obtained from each of one or several closely related populations or species.
FAMD (Fingerprint Analysis with Missing Data) is an easy-to-use general-purpose program for dominant fingerprint data handling and analysis (explicitly allowing ambiguities/missing data points) with a graphical user interface, supporting flexible data input and export to a variety of formats. Analysis capabilities include distance-based analysis (trees and PCoA, with graphical 3D viewer), bootstrapping and consensus tree generation, allele frequency estimation, AMOVA, inter-population distances, Shannon’s index.
The VAMP software (Visualization and Analysis of array-CGH, transcriptome and other Molecular Profiles)allows the visual comparison of the array-CGH profiles of a cohort of patients, or the confrontation of array-CGH, expression and loss of heterozygosity profiles. VAMP offers many functionalities such as computing recurrent alterations, clustering profiles, crossing with clinical or biological annotations, performing syntenic projection onto the genome of another species.
The Gene Construction Kit®(GCK) program has been the preferred plasmid mapping software of leading researchers for more than 20 years. GCK allows easy manipulation of DNA sequences, either graphically or as sequence text – quickly saving users both time and money. GCK eliminates tedious examination of DNA sequence data by automatically identifying open reading frames (ORF’s), keeping track of sticky ends during cutting and pasting of restriction enzyme digestion fragments, assisting with PCR primer design, and enabling comprehensive annotation of DNA sequence features. This DNA analysis software allows multiple files to be opened and displayed simultaneously, allowing DNA sequences to easily be copied and pasted between plasmids and vectors to represent real-world DNA cloning protocols. The Gene Construction Kit software is available for both Windows and Macintosh users, and files can be shared across platforms allowing for easy collaboration.
MEGA （Molecular Evolutionary Genetics Analysis）is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.