T-Rex (Tree and reticulogram REConstruction) - is dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks (Reference: Alix, C. et al. 2012. Nucl. Acids Res. 40 (W1): W573-W579).
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). Also available here.
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: Guindon, S.et al. 2010. Systematic Biology, 59(3):307-21).
RAxML (Randomized Axelerated Maximum L ikelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees (Reference: Stamatakis, A. 2006. Bioinformatics 22:2688–2690).
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.
Phylemon2 - a suite of web-tools for molecular evolution, phylogenetics and phylogenomics (Reference:Sánchez, R. et al. 2011.Nucl. Acids Res. 39/suppl_2/W470)
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)
Phylogenetic Tree Plot (Laboratory of Bioinformatics, Wageningen UR, The Netherlands) - submit tree descriptions in PHYLIP (Newick) format only
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)
webPRANK - incorporates phylogeny-aware multiple sequence alignment, visualisation and post-processing in an easy-to-use web interface.(Reference: Löytynoja, A., & Goldman, N. 2010. BMC Bioinformatics. 11:579).
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles - they used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on the new web server, PhyloGene. (Reference: I.R. Sadreyev et al. 2015. Nucl. Acids Res. 43 (W1): W154-W159).
SIFTER (Statistical Inference of Function Through Evolutionary Relationships) is a statistical approach to predicting protein function that uses a protein family's phylogenetic tree, as the natural structure for representing protein relationships. (Reference: S.M. Sahraeian et al. 2015. Nucl. Acids Res. 43 (W1): W141-W147).
ReplacementMatrix - maximum-likelihood estimation of amino acid replacement rate matrices.(Reference: Dang, C.C. et al. 2011. Bioinformatics. 27(19):2758-2760).
DIVEIN - starting with a set of aligned sequences, DIVEIN estimates evolutionary parameters and phylogenetic trees while allowing the user to choose from a variety of evolutionary models; it then reconstructs the consensus (CON), most recent common ancestor (MRCA), and center of tree (COT) sequences. DIVEIN also provides tools for further analyses. (Reference: Deng, W. et al. 2010. Biotechniques. 48(5):405-408).
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
AmphoraNet - is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample; the webserver is based on the AMPHORA2 workflow. It uses 31 bacterial and 104 archaeal protein coding marker genes for metagenomic phylotyping. Most of these are single copy genes, therefore AmphoraNet is suitable for estimating the taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data. (Reference: Kerepesi, C. et al. 2014. Gene 533: 538–540)
GGDC - Genome-to-Genome Distance Calculator - The species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). This web service can be used for genome-based species delineation with complete or incomplete genomes sequences. The server calculate intergenomic distances; and, these are converted into similarity values analogous to DDH and sent to you via e-mail. (Reference: Meier-Kolthoff, J.P. et al. 2013. BMC Bioinformatics 14:60).
VICTOR (Virus Classification and Tree Building Online Resource; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH). This web service compares bacterial and archaeal viruses ("phages") using their genome or proteome sequences. The results include phylogenomic trees inferred using the Genome-BLAST Distance Phylogeny method (GBDP), with branch support, as well as suggestions for the classification at the species, genus and family level. (The service can be applied to other kinds of viruses, too, but has not yet been tested in this respect.) Upload your FASTA files, GenBank files and/or GenBank accession IDs.
MyTaxa - represents a new algorithm that extends the Average Amino Acid Identity (AAI) concept to identify the taxonomic affiliation of a query genome sequence or a sequence of a contig assembled from a metagenome, including short sequences, and to classify sequences representing novel taxa at three levels i.e., species, genus and phylum. MyTaxa can assign a larger number of sequences and with higher accuracy compared to other tools available for the same purposes. This is largely attributed to the fact that MyTaxa considers all genes present in an unknown (query) sequence as classifiers and quantifies the classifying power of each gene using predetermined weights, which are derived from the analysis of orthologs of the gene from all available complete genomes. (Reference: Luo, C. et al. 2014. Nucl. Acids Res).
ANI calculator - estimates the average nucleotide identity using both best hits (one-way ANI) and reciprocal best hits (two-way ANI) between two genomic datasets. Typically, the ANI values between genomes of the same species are above 95% while values below 75% are not to be trusted, and AAI should be used instead. This tool supports both complete and draft genomes (multi-fasta).(Reference: Goris J. et al. 2007. Int J Syst Evol Microbiol. 57:81-91).
TaxMan: Inspect your rRNA amplicons and taxa assignments - In microbiome analyses, often rRNA gene databases are used to assign taxonomic names to sequence reads. The TaxMan server facilitates the analysis of the taxonomic distribution of your reads in two ways. First, you can check what taxonomic names are assigned to the sequences produced by your primers and what taxa you will lose. Second, the produced amplicon sequences with lineages in the FASTA header can be downloaded. This can result in a much more efficient analysis with respect to run time and memory usage, since the amplicon sequences are considerably shorter than the full length rRNA gene sequences. In addition, you can download a lineage file that includes the counts of all taxa for your primers and for the used reference. (Reference: Brandt, B.W. et al. 2012. Nucleic Acids Research 40:W82-W87).