Table 6

It refers to analysis that each package can by itself perform irrespective of whether it can receive as input results produced from another tool for a specific category of analysis.

Bio* and Open-source projects: limited or no visualization

Project

Comments

R

Interfaces all major prog. languages, such as MATLAB, Perl, Python, Java, C, C++ and Fortran; wide bioinformatics, statistical and clustering analysis possibilities.

Bioconductor

Relies on R; appropriate towards statistical analysis of microarray experiments.

BioPerl

Relies on Perl; phylogenetic analysis, multiple sequence alignment and microarray analysis are facilitated; well-established interfaces to other prog. languages.

BioJava

Relies on java; mainly sequence analysis; low compatibility with other languages and limited functionalities compared to BioPerl.

BioPython, BioRuby, BioBike, BioLisp

Reliance on Python, Ruby, BioLisp, Lisp respectively; apart from the main sequence alignment, among others, microarray analysis is available too.

Pavlopoulos et al. BioData Mining 2010 3:1   doi:10.1186/1756-0381-3-1