Phylogeny

HyPhy

HyPhy - intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more.

Reference: S.L. Kosakovsky et al.(2005) Bioinformatics 21:676-679.

ChromaClade

ChromaClade - is a convenient tool with a graphical user-interface that works in concert with popular tree viewers to produce colour-annotated phylogenies highlighting residues found in each taxon and at each site in a sequence alignment. Colouring branches according to residues found at descendent tips also quickly identifies lineage-specific residues and those internal branches where key substitutions have occurred.

Reference: Monit C et al. (2019) BMC Evol Biol 19: 186.

Treefinder

Treefinder (Gangolf Jobb, Statistical Genetics and Bioinformatics, University of Munich) computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method, it is offering a variety of evolutionary models up to the general time reversible model with Gamma and codon position rate heterogeneity among sites. The confidence of inferred relationships may be assessed by bootstrap analysis or, alternatively, by a local rearrangement paired-sites method (LRP). Linus and Mac versions also available.

MEGA

MEGA - an incredible phylogenetic analysis program.

Reference: S. Kumar et al. (2001) Bioinformatics 17: 1244-1245.

Tree-Puzzle

Tree-Puzzle (H.A. Schmidt, K. Strimmer, M. Vingron, & A. von Haeseler, Germany) constructs phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.

PHYLIP

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies. PHYLIP is the most widely-distributed phylogeny package, and competes with PAUP to be the one responsible for the largest number of published trees (Joe Felsenstein, University of Washington, U.S.A.).

MrBayes

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints.

PAML

PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.

NJplot

NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Reference: Perrière, G. & Gouy, M. (1996) Biochimie, 78: 364-369.

Orthologous Average Nucleotide Identity Tool (OAT)

Orthologous Average Nucleotide Identity Tool (OAT) - OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments.

Reference: Lee, I. et al. (2015). Int J Syst Evol Microbiol. 66: 1100-1103.