Phylemon runs distance-based methods, maximum parsimony analyses and statistical methods of phylogenetic reconstruction. Distances and parsimony methods for DNA or protein sequence data are provided by the most often used algorithms of the PHYLIP package (2
) v3.65: DnaDist, ProtDist, DnaPars and ProtPars, respectively. Pairwise distance matrices can be represented in a phylogenetic tree using the neighbor-joining (NJ) algorithm (Neighbor) or applying a least square (LS) method or a minimum evolution (ME) criterium (Fitch program). In order to obtain trees with statistical support on internal nodes, a re-sampling method (i.e. bootstrap option included in the Seqboot algorithm) and the corresponding trees summarizing algorithm (i.e. majority rule tree using Consense program) of PHYLIP are included.
Basic maximum likelihood (ML) analyses of DNA and protein sequence data are provided with the DnaML and ProML algorithms of the PHYLIP package in Phylemon. When a more sophisticated ML analysis is required users can run PhyML version aLRT (9
) or TREE-PUZZLE v5.2 (11
). Major differences between these ML programs are: (1) PhyML is faster than any other ML algorithm of phylogenetic reconstruction, (2) TREE-PUZZLE uses a quartet-puzzling method instead the more classical heuristic searches for tree searching, (3) TREE-PUZZLE reports reliability values while the PhyML method reports Felsenstein's bootstrap values and aLRT-related statistics branch support (9
), (4) TREE-PUZZLE can quantify the amount of the phylogenetic signal contained in a data set (the probability of the data producing a tree-like phylogenetic representation) through the likelihood-mapping method (12
) and (5) TREE-PUZZLE computes ML pairwise distances that can easily be represented in an NJ/LS/ME tree.
Finally, Phylemon runs Bayesian phylogenetic analysis using MrBayes v3.1.12 (6
). MrBayes runs in Phylemon with the same characteristics that users have in Windows or Linux interfaces. Users can define all the parameters of MrBayes in a file to upload to the server or, alternatively, edit the parameters in the specific text box when entering the data. A valuable list of examples showing alternative data and parameters is available in the server. In addition, when users edit sequence data or parameters, the MrBayes command list is available on the fly. At the end of the run, Phylemon asks for the sump and sumt parameters in order to define the burnin limit (D). Once the analysis is finished, 10 outfiles are listed, 8 corresponding to the usual files produced by MrBayes and 2 corresponding to: (1) all information printed to the standard output the program runs (outfile.out) and (2) the last topologies retained (with branch lengths and posterior probabilities on the nodes—tree.nw), the last of which can be visualized in a tree-viewer program available in the utilities section of Phylemon.