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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.

From: A reference guide for tree analysis and visualization

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.