Phylemon is the suite of web-tools for molecular evolution, phylogenetics and phylogenomics. It is conceived as a natural response to the increasing demand of data analysis of experimental scientists seeking to add molecular evolution and phylogenetic insight into their research.
SDM (super distance matrix ) is a new method to combine distance matrices (or trees with branch lengths). This method involves deforming the different matrices, without modifying their topological message, to bring them as close as possible to each other. A distance supermatrix is then computed by averaging the deformed source matrices. When this supermatrix is complete, any tree building algorithm can be used to obtain the supertree that summarizes the input distance matrices (or trees with branch lengths); e.g. BioNJ or FastME (recommended).
OrthoSelect is a easy-to-install and easy-to-use tool for finding ortholog groups in EST databases. It automatically searches assembled EST sequences against databases of ortholog groups (OG), assigns ESTs to these pre-defined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified ortholog sequences and others the possibility to further process this alignment in a last step. OrthoSelect performes better than the best-hit selection strategy and shows reliable results re-annotating database member sequences of OrthoMCL-DB and KOG. Since a correct orthology assignment is a important prerequisite for the construction of reliable data sets, OrthoSelect is capable of producing such data sets. This makes a OrthoSelect a valuable tool for researcher dealing with large EST libraries focussing on constructing data sets for phylogenetic reconstructions.