PHYLOGENY

Phylip on the Web (L'Institute Pasteur, France) - for information on this set of programs see: Joseph Felenstein, (University of Washington, U.S.A.).

 Phylogeny.fr - is a simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.It includes multiple alignment (MUSCLE, T-Coffee, ClustalW, ProbCons), phylogeny (PhyML, MrBayes, TNT, BioNJ), tree viewer (Drawgram, Drawtree, ATV) and utility programs (e.g. Gblocks to eliminate poorly aligned positions and divergent regions) (Reference: A. Dereeper  et al,. 2008. Nucl. Acids Res. 36 (Web Server Issue):W465-9).

PHYML - is a simple, fast and accurate algorithm to estimate maximum likelihood phylogenies from DNA and protein sequences. This tool provides the user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters. (Reference: S. Guindon et al. 2005. Nucl. Acids Res. 33: W557-W559).
ProtTest (David Posada, University of Vigo, Spain) - estimates the empirical model of aminoacid substitution that fits the data best among 64 candidate models. PROTTEST calculates AIC, AICc and BIC values, and obtain a rank of model fits, model-averaged parameter estimates, or measures of parameter importance.  Mac OSX, Windows and Linux versions are available for downloading.

 Phylemon - a suite of web-tools for molecular evolution, phylogenetics and phylogenomics (H. Dopazo. Bioinformatics Department, Centro de Investigación Príncipe Felipe, Spain)

POWER (PhylOgenetic Web Repeater) - allows users to carry out phylogenetic analysis on most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the beginning of the pipeline whereas the other begin phylogenetic analysis with aligned sequence. Very user friendly. (Reference: C.-Y. Lin. et al. 2005. Nucl. Acids Res. 33: W553-W556).
Phylodendron - phylogenetic tree printer (D.G. Gilbert, Indiana Univ.) - very useful in visualizing *.dnd file from aligments and saving the results as .GIF, .PS or .PDF files.  N.B. The font style and size can be altered in the .PDF output format.
Phylogenetic tree prediction - GeneBee service (Belozersky Institute of Physico-chemical Biology, Moscow State University, Russia)

LVB: Reconstructing Evolution with Parsimony and Simulated Annealing (Pasteur Institute, France) - "LVB uses unweighted reversible parsimony to reconstruct evolution based on a matrix of discrete characters for different objects such as aligned DNA sequences.  To find parsimonious trees, LVB uses the heuristic search known as simulated annealing." For details see the developer's (Daniel Barker) site.

 CVTree - Composition Vector - constructs whole-genome based phylogenetic trees without sequence alignment by using a Composition Vector (CV) approach. It was first developed to infer evolutionary relatedness of microbial organisms and then successfully applied to viruses, chloroplasts, and fungi. It circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. (Reference: Z. Xu & B. Hao 2009. Nucl. Acids Res. 37(Web Server issue:W174-W178)

Ribosomal RNA Analysis - The Ribosomal Database Project II (Michigan State University Centre for Microbial Ecology, U.S.A.).
Ridom - Ribosomal RNA analysis for clinically relevant bacteria - (University of Würzburg, Germany)
Rifle - (Universitat Bielefeld, Germany) The RIFLE system compares restriction patterns of 16S rDNA amplicons against a database of theoretical restriction patterns generated from a 16S rDNA database