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MrBayes
Estimates the posterior distribution of model parameters. MrBayes is a program that performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo (MCMC). It can infer ancestral states while accommodating uncertainty about the phylogenetic tree and model parameters. It also implements several methods for relaxing the assumption of equal rates across sites, including gamma-distributed rate variation. It can be used to test various topological hypotheses or substitution models against each other.
PAML / Phylogenetic Analysis by Maximum Likelihood
A package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). PAML may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations.
BEAST / Bayesian Evolutionary Analysis by Sampling Trees
A cross-platform program for Bayesian phylogenetic analysis of molecular sequences. BEAST estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. It uses an XML input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.
SATe / Simultaneous Alignment and Tree Estimation
Involves repeated alignment and tree searching operations. SATé is a software package for inferring a sequence alignment and phylogenetic tree. It searches for a tree/alignment pair with an optimal maximum likelihood (ML) score by performing hill-climbing searches from a collection of starting tree/alignment pairs. For each starting alignment, SATé estimates an ML tree (general time reversible + gamma model) with RAxML. The “second stage” then uses an iterative, greedy search heuristic to find tree/alignment pairs with better ML scores.
IQ-TREE
Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
PHYLIP / the PHYLogeny Inference Package
A free package of programs for inferring phylogenies. It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It also computes consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. PHYLIP handles data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters, and continuous characters.
CVTree / Composition Vector Tree
An implementation of the whole genome-based, alignment-free composition vector (CV) method for phylogenetic analysis. Users can upload their own sequences to find their phylogenetic position among genomes selected from the server's; inbuilt database. All sequence data used in a session may be downloaded as a compressed file. In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels. This feature is particularly useful for comparing phylogeny with taxonomy when dealing with thousands of genomes.
FastME
Provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server.
PHAST / PHylogenetic Analysis with Space/Time models
Allows statistical phylogenetic modeling and functional element identification. PHAST is a collection of programs and supporting libraries for comparative genomics. The software also provides methods for detecting departures from neutrality in rates and patterns of molecular evolution. It is well-suited for analyzing patterns of conservation and acceleration in aligned sequences, and for extracting data from or exporting data to the UCSC Genome Browser and related resources, such as Galaxy.
Bio++
Provides a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Bio++ provides built-in access to sequence databases and data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.
Stacks
Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core population genomic summary statistics and single nucleotide polymorphism (SNP)-by-SNP statistical tests. It aims to be a key resource to empower researchers to efficiently perform ecological and evolutionary genomic studies in model organisms and particularly in organisms with minimal or no genomic resources.
PyRate
Estimates speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. Pyrate includes several methods to understand how rates vary through time and whether they correlate with traits (e.g. body size) or respond to continuous variables (e.g. climate proxies) or competitive effects (through diversity dependence). Macro evolutionary rates are jointly estimated with preservation rates, describing processes of fossilization, sampling and identification of organisms.
TransPhylo
A Matlab package based on a Bayesian inference method for reconstructing transmission events in a densely sampled outbreak using time-labeled genomic data. TransPhylo works by colouring the branches of the phylogeny using a separate colour for each host, sampled or not. Each section of the tree coloured in a unique colour represents the pathogen evolution happening within a distinct host. Changes of colours on branches therefore correspond to transmission events from one host to another. Authors conclude that genomics cannot wholly replace traditional epidemiology but that Bayesian reconstructions derived from sequence data may form a useful starting point for a genomic epidemiology investigation.
Gubbins / Genealogies Unbiased By recomBinations In Nucleotide Sequences
Identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Gubbins uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer. Gubbins is also a practical tool in the context of current sequencing capacity; it is typically able to converge on a result for an alignment of 100 two megabase sequences in well under an hour, whereas others sophisticated model fitting can take weeks to analyze a much smaller number of genomes.
ProtEvol
Generates independent site-specific amino acid distributions. ProtEvol uses constraints on the stability of the native state against both unfolding and misfolding, and depends on a background distribution of amino acids and one user-fixed selection parameter maximizing the likelihood of the observed protein sequence. It also simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.
PhyloGenie
A Perl script combining the various steps necessary to producing a phylome. PhyloGenie sets up a list of programs that automates the steps from seed sequence to phylogeny and a utility to extract all phylogenies that match specific topological constraints from a database of trees. BLAST or PSI-BLAST searches are performed for all input sequences, the HSP's (High Scoring Pairs) corresponding to user defined selection criteria (E-value, coverage, score per column, identity) are extracted and used as a basis for multiple sequence alignment.
STRAW / Species TRee Analysis Web server
A web server that offers workflows for reconstruction of phylogenies of species using three species tree methods-MP-EST, STAR and NJst. The input data are a collection of rooted gene trees (for STAR and MP-EST methods) or unrooted gene trees (for NJst). The output includes the estimated species tree, modified Robinson-Foulds distances between gene trees and the estimated species tree and visualization of trees to compare gene trees with the estimated species tree.
POWER / the PhylOgenetic WEb Repeater
Conducts phylogenetic analysis of protein and nucleic acid sequences. POWER conducts MSA and phylogenetic analysis thanks to algorithms from ClustalW and the PHYLIP package. Its system separates a job into two modes: “user mode”, allowing users to manipulate all the parameters for MSA and phylogenetic analysis and view the results on a web browser; (2) and “system mode”. This tool integrates features for parallel calculation and an optimized database structure for parameter collection, job processing and result visualization.
MUST / Management Utilities for Sequences and Trees
New
Manages all the operations needed for phylogenetic reconstructions. MUST can deal with both raw data in form of sequences and results such as trees, number of steps or bootstrap proportions. It provides the following parts: (1) acquisition, storage, modification and checking of molecular data; (2) sequence editing and aligning; (3) selection of data for phylogenetic reconstruction; and (4) critical analysis of the phylogenetic deductions. This tool permits reformulation of phylogenetic problems and assessment of the quality of the sequence sampling.
TreeSimGM
A flexible simulation tool for phylogenetic trees under a general model. TreeSimGM can assume any probability distribution for the waiting time until speciation and extinction independently. Thus, TreeSimGM allows to simulate stochastic phylogenetic trees using any probability distribution and parameters for speciation and extinction. The speciation modes have all binary splits and are: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. Those two modes were inspired by allopatric and peripatric speciation respectively.
TreeSim
Simulates trees with a fixed number of extant species. TreeSim is a constant rate birth-death process with mass extinction and/or rate shift events at arbitrarily fixed times 1) before the present or 2) after the origin. The simulation approach for case (2) can also be used to simulate under more general models with fixed events after the origin. I use the developed simulation tools for showing that a mass extinction event cannot be distinguished from a model with constant speciation and extinction rates interrupted by a phase of stasis based on trees consisting of only extant species.
TIGER / Tree Independent Generation of Evolutionary Rates
Identifies rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). TIGER can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted in order to improve phylogenetic reconstruction. When a site is changing very quickly between taxa it might not hold much phylogenetic information and therefore might simply be a source of noise. Use of TIGER can (a) allow you to see the amount of rapid evolution and noise in your alignment and (b) provide a quick and easy way to remove as many of the “noisy” sites as possible.
Phycas
A python extension for phylogenetic analysis. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used Harmonic Mean estimator. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length.
ghost-tree
A bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child.
GEIGER
Describes evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Its main purpose is to detect and describe evolutionary radiations. Additionally, GEIGER’s simulation algorithms can be used to analyze the statistical power of comparative approaches. It can simulate both phylogenetic trees and phenotypic characters and also permits several types of tree pruning that are central to phylogenetic comparative analyses. To facilitate comparison between simulated trees (which include both extinct and extant taxa) and actual phylogenies (which typically include only extant taxa), GEIGER permits the pruning of extinct lineages.
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