%0 Journal Article
%T Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
%A Julien Pel¨¦
%A Jean-Michel B¨¦cu
%A Herv¨¦ Abdi
%A Marie Chabbert
%J BMC Bioinformatics
%D 2012
%I BioMed Central
%R 10.1186/1471-2105-13-133
%X The R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. ¡°out of sample¡± elements) onto the space defined by reference or ¡°active¡± elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families.The bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.
%K Metric multidimensional scaling (MDS)
%K Principal coordinate analysis
%K R program
%K Supplementary elements
%K Evolution
%K Protein family
%K Phylogeny
%U http://www.biomedcentral.com/1471-2105/13/133/abstract