Sequence clustering with PaSiMap in Jalview

Pairwise similarity mapping, implemented in the software PaSiMap, can be used as an alternative to principal component analysis (PCA) to analyse protein-sequence relationships. It provides the advantage of distinguishing between systematic and random differences in the dataset. Here, we present a protocol to use PaSiMap inside Jalview. You will be guided through the installation and use of the required software. Furthermore, we present an R script to prepare publication-ready graphs of the obtained data and aid in the subsequent data analysis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/621149v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1daf3d2org.highwire.dtl.DTLVardef@1bd82cborg.highwire.dtl.DTLVardef@d60c7aorg.highwire.dtl.DTLVardef@cd5a89_HPS_FORMAT_FIGEXP M_FIG C_FIG