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Phylogenetic inference software tools | Phylogenomics

The task of resolving the tree of life of extant species remains one of the grand challenges in evolutionary biology. As the number of trees grows superexponentially with the number of species for which an evolutionary tree is reconstructed, tree…
PhyloPat
Dataset

PhyloPat

Allows the complete Ensembl gene database to be queried using phylogenetic…

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…

Phylogeny.fr
Web

Phylogeny.fr

Allows to reconstruct and analyse phylogenetic relationships between molecular…

Allows to reconstruct and analyse phylogenetic relationships between molecular sequences. Phylogeny.fr is composed of (1) a pipeline to reconstruct a phylogenetic tree from a set of sequences through…

RAxML
Desktop

RAxML Randomized Axelerated Maximum Likelihood

A popular program for phylogenetic analyses of large datasets under maximum…

A popular program for phylogenetic analyses of large datasets under maximum likelihood.

tree-puzzle
Desktop

tree-puzzle

Reconstructs phylogenetic trees from molecular sequence data by maximum…

Reconstructs phylogenetic trees from molecular sequence data by maximum likelihood. TREE-PUZZLE is a computer program allows analysis of large data sets and automatically assigns estimations of…

TransPhylo
Desktop

TransPhylo

A Matlab package based on a Bayesian inference method for reconstructing…

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…

SATe
Desktop

SATe Simultaneous Alignment and Tree Estimation

Involves repeated alignment and tree searching operations. SATé is a software…

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…

IQ-TREE
Web
Desktop

IQ-TREE

Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores…

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…

RevBayes
Desktop

RevBayes

Provides an interactive environment for statistical computation in…

Provides an interactive environment for statistical computation in phylogenetics. RevBayes is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly…

RWTY
Desktop

RWTY R We There Yet

Implements various tests, visualizations, and metrics for diagnosing…

Implements various tests, visualizations, and metrics for diagnosing convergence and mixing of Markov chain Monte Carlo (MCMC) chains in phylogenetic. RWTY implements and automates many of the…

POPTREEW
Web
Desktop

POPTREEW

A web app for evolutionary analyses of allele frequency data. POPTREEW can…

A web app for evolutionary analyses of allele frequency data. POPTREEW can compute various types of genetic distance and construct phylogenetic trees of populations using the neighbor-joining method…

FastME
Web
Desktop

FastME

Provides distance algorithms to infer phylogenies. FastME is based on balanced…

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…

sampletrees/Rsa…
Desktop

sampletrees/Rsampletrees

A Markov chain Monte Carlo sampler of gene genealogies conditional on either…

A Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees…

CSI Phylogeny
Web

CSI Phylogeny Call SNPs & Infer Phylogeny

Identifies variations in whole genome sequencing (WGS) reads and conducts…

Identifies variations in whole genome sequencing (WGS) reads and conducts phylogenetic analysis of isolates. CSI Phylogeny is a webserver which calls and filters the single nucleotide polymorphisms…

ExaBayes
Desktop

ExaBayes

A user-friendly software package engineered for conducting state-of-the-art…

A user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size. ExaBayes introduces a nonblocking parallelization of…

rRNA phylogeny
Desktop

rRNA phylogeny

Allows phylogenetic analyses (using Phylip) of ribosomal RNA (rRNA). rRNA…

Allows phylogenetic analyses (using Phylip) of ribosomal RNA (rRNA). rRNA phylogeny uses a matrix of empirical substitution rates and the OTRNA model. This method allows to obtain a large number of…

PHAST
Desktop

PHAST PHylogenetic Analysis with Space/Time models

A freely available software package for comparative and evolutionary genomics.…

A freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments,…

phydms
Desktop

phydms Phylogenetic analyses using Deep Mutational Scanning

Enables phylogenetic analyses using deep mutational scanning data to inform the…

Enables phylogenetic analyses using deep mutational scanning data to inform the substitution models. Phydms uses the Experimentally Informed Codon Models (EICM) which describes the evolution of…

TESS
Desktop

TESS

Allows users to specify an effectively countless number of diversification…

Allows users to specify an effectively countless number of diversification models, where each model describes an alternative scenario for the diversification of the three. TESS can be used to…

VMCMC
Desktop

VMCMC

Simplifies post-processing of MCMC traces with, for example, automatic burn-in…

Simplifies post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC, a tool for phylogenetic MCMC analysis, with support for analysis and exploration of chain…

DiscoMark
Desktop

DiscoMark

Discovers phylogenetic markers from orthologous sequences. DiscoMark is a…

Discovers phylogenetic markers from orthologous sequences. DiscoMark is a bioinformatics program designed to make it easy to develop phylogenetic markers from orthologous DNA sequences. One of the…

PLL
Desktop

PLL Phylogenetic Likelihood Library

An application programming interface for developing likelihood-based…

An application programming interface for developing likelihood-based phylogenetic inference and post analysis software. The PLL package implements appropriate data structures and functions that allow…

Phycas
Desktop

Phycas

A python extension for phylogenetic analysis. Phycas specializes in Bayesian…

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…

ProtEvol
Desktop

ProtEvol

Generates independent site-specific amino acid distributions. ProtEvol uses…

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…

MixTreEM
Desktop

MixTreEM Mixture of Trees using Expectation Maximization

A package to reconstruct species tree. MixTreEM uses a probabilistic generative…

A package to reconstruct species tree. MixTreEM uses a probabilistic generative mixture model to reconstruct a set of k-candidate species trees given a set of n monocopy gene families. In the first…

BayesCAT
Desktop

BayesCAT Bayesian Co-estimation of Alignment and Tree

Implements a joint model for co-estimating phylogeny and sequence alignment.…

Implements a joint model for co-estimating phylogeny and sequence alignment. The BayesCAT software allows arbitrary-length overlapping indel events and a general distribution for indel fragment size.…

PyRate
Desktop

PyRate

Estimates speciation, extinction, and preservation rates from fossil occurrence…

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…

GGDC
Web

GGDC Genome-To-Genome Distance Calculator

Offers a methods for deducing whole-genome distances which are able to mimic…

Offers a methods for deducing whole-genome distances which are able to mimic DDH (DNA-DNA hybridization). GGDC can serve for genome-based species delineation and genome-based subspecies delineation.…

PrIME-GSR
Desktop

PrIME-GSR

Unifies sequence evolution models and substitution rate evolution models.…

Unifies sequence evolution models and substitution rate evolution models. PrIME-GSR allows users to design a biologically realistic method to reconstruct a gene tree, in the sense that the processes…

Co-phylog
Desktop

Co-phylog

Creates a micro-alignment in a sequence using the context of an object.…

Creates a micro-alignment in a sequence using the context of an object. Co-phylog is a phylogenomic approach that takes advantage of unassembled next-generation sequencing (NGS) data from complete…

nsSNPCounter
Web

nsSNPCounter

Allows analysis of synonymous and non-synonymous codon substitutions in protein…

Allows analysis of synonymous and non-synonymous codon substitutions in protein coding genes. nsSNPCounter can estimate the number of synonymous (SynSites) and non-synonymous (NonSynSites) sites…

VICTOR
Web

VICTOR Virus Classification and Tree Building Online Resource

Compares bacterial and archaeal viruses using their genome or proteome…

Compares bacterial and archaeal viruses using their genome or proteome sequences. The VICTOR results include phylogenomic trees inferred using the Genome-BLAST Distance Phylogeny method (GBDP), with…

ghost-tree
Desktop

ghost-tree

A bioinformatics tool that integrates sequence data from two genetic markers…

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"…

phyloSkeleton
Desktop

phyloSkeleton

Selects the most representative organisms, following a set of simple rules…

Selects the most representative organisms, following a set of simple rules based on taxonomy and assembly quality. phyloSkeleton allows users to retrieve the genomes from public databases (NCBI,…

ALFRED-G
Desktop

ALFRED-G

Solves the generalized common substring search problem via exact computation.…

Solves the generalized common substring search problem via exact computation. ALFRED-G is an alignment free distance estimator software for phylogenetic inference. This heuristic has been further…

ERaBLE
Desktop

ERaBLE Evolutionary Rates and Branch Length Estimation

A phylogenomic distance-based method to estimate the branch lengths of a given…

A phylogenomic distance-based method to estimate the branch lengths of a given reference topology, and the relative evolutionary rates of the genes employed in the analysis. ERaBLE uses as input data…

FastTree
Desktop

FastTree

Constructs large phylogenies and estimates their reliability. FastTree uses…

Constructs large phylogenies and estimates their reliability. FastTree uses nearest-neighbor interchanges (NNIs), the minimum-evolution criterion, minimum-evolution subtree-pruning-regrafting (SPRs)…

AAF
Desktop

AAF Alignment and Assembly Free

Provides an efficient way of estimating the phylogenetic relationships using…

Provides an efficient way of estimating the phylogenetic relationships using raw sequence data from whole genomes. The AAF method is a robust tool for phylogeny reconstruction especially when only…

MrBayes
Desktop

MrBayes

Estimates the posterior distribution of model parameters. MrBayes is a program…

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…

ChromEvol
Desktop

ChromEvol

Infers the pattern of chromosome number change along a phylogeny. ChromEvol…

Infers the pattern of chromosome number change along a phylogeny. ChromEvol facilitates the inference of the expected number of polyploidy and dysploidy transitions along each branch of a phylogeny…

REALPHY
Desktop
Web
PAML
Desktop

PAML Phylogenetic Analysis by Maximum Likelihood

A package of programs for phylogenetic analyses of DNA and protein sequences…

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…

GNT
Desktop

GNT Genome Topology Network

A method based on gene homology and gene locations to analyse genomic single…

A method based on gene homology and gene locations to analyse genomic single variations (SVs) and perform phylogenetic analysis. GNT allows re-annotating missing genes among closely related genomes,…

Bio++
Desktop

Bio++

Provides a set of C++ libraries for Bioinformatics, including sequence…

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…

OGtree
Web

OGtree

Constructs genome trees of prokaryotic species based on a measure of combining…

Constructs genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. OGtree utilizes distance-based methods of…

Gubbins
Desktop

Gubbins Genealogies Unbiased By recomBinations In Nucleotide Sequences

Identifies loci containing elevated densities of base substitutions while…

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…

PhyloGenie
Desktop

PhyloGenie

A Perl script combining the various steps necessary to producing a phylome.…

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…

RSAT…
Web

RSAT matrix-clustering

Supports dynamic browsing of motif trees with custom collapse/expansion of…

Supports dynamic browsing of motif trees with custom collapse/expansion of branches. RSAT matrix-clustering also provides multiple ways to inspect the results: motif forest with branch motifs at each…

TreeExp
Desktop

TreeExp

Performs comparative expression evolution analysis based on RNA-seq data.…

Performs comparative expression evolution analysis based on RNA-seq data. TreeExp includes optimized input formatting, normalization, pairwise expression distance estimation, expression character…

bModelTest
Desktop

bModelTest bayesian Model Test

A Bayesian model test package for BEAST2. bModelTest can be used in any…

A Bayesian model test package for BEAST2. bModelTest can be used in any analysis where trees are estimated based on nucleotide sequences, such as multi-species coalescent analysis, various forms of…

Phylo-Node
Desktop

Phylo-Node

Allows the user to go from sequence retrieval to phylogeny reconstruction.…

Allows the user to go from sequence retrieval to phylogeny reconstruction. Phylo-Node can execute the analysis and process the resulting outputs from a suite of software options that provides tools…

HOGAN
Desktop

HOGAN

Designed to obtain an efficient sampling of parameter-rich and complex models.…

Designed to obtain an efficient sampling of parameter-rich and complex models. HOGAN is a parallel Metropolis-Hastings (M-H) framework built with a combination of enhancements aimed towards…

CloudPhylo
Desktop

CloudPhylo

A fast and scalable Spark-based tool for reconstruction of phylogenetic tree…

A fast and scalable Spark-based tool for reconstruction of phylogenetic tree from large-scale datasets. CloudPhylo is capable of efficiently and effectively dealing with big data and achieving good…

MultiTypeTree
Desktop

MultiTypeTree

Capables of sampling from posterior distributions over structured trees.…

Capables of sampling from posterior distributions over structured trees. MultiTypeTree provides means of using serially sampled sequence data to infer the full structured tree and related model…

PUmPER
Desktop

PUmPER Phylogenies Updated PERperpetually

A framework to build automated pipelines that can perpetually update…

A framework to build automated pipelines that can perpetually update phylogenetic trees. PUmPER makes use of PHLAWD and RAxML-Light or ExaML to perpetually update Genbank datasets and simultaneously…

ASTRAL
Desktop

ASTRAL Accurate Species TRee ALgorithm

A Java program for estimating a species tree given a set of unrooted gene…

A Java program for estimating a species tree given a set of unrooted gene trees. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed ‘bipartitions’. ASTRAL-II…

Kdetrees
Desktop

Kdetrees

A non-parametric method for estimating distributions of phylogenetic trees,…

A non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

MEGA
Desktop

MEGA Molecular Evolutionary Genetics Analysis

An integrated tool for conducting sequence alignment, inferring phylogenetic…

An integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral…

compat
Desktop

compat

Rapidly computes phylogenies according to a compatibility criterion. Although…

Rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, compat deals properly with ambiguities in the data. The algorithm is…

RPHAST
Desktop

RPHAST R PHylogenetic Analysis with Space/Time models

A package for many types of analysis in comparative and evolutionary genomics.…

A package for many types of analysis in comparative and evolutionary genomics. RPHAST can estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and…

TIGER
Desktop

TIGER Tree Independent Generation of Evolutionary Rates

Identifies rapidly evolving sites (columns in an alignment, or characters in a…

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…

TreeSimGM
Desktop

TreeSimGM

A flexible simulation tool for phylogenetic trees under a general model.…

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,…

TreeSim
Desktop

TreeSim

Simulates trees with a fixed number of extant species. TreeSim is a constant…

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…

PhyML
Desktop

PhyML

Estimates maximum likelihood phylogenies from alignments of nucleotide or amino…

Estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequence. PhyML is a phylogeny software based on the maximum-likelihood principle. It implements algorithms to…

sampled-ancesto…
Desktop

sampled-ancestors

Infers trees in which sampled individuals can be direct ancestors of other…

Infers trees in which sampled individuals can be direct ancestors of other sampled individuals. This method allows the detection of sampled ancestors as well as the estimation of the probability that…

PHYLIP
Desktop

PHYLIP the PHYLogeny Inference Package

A free package of programs for inferring phylogenies. It can infer phylogenies…

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…

BEAST
Desktop

BEAST Bayesian Evolutionary Analysis by Sampling Trees

A cross-platform program for Bayesian phylogenetic analysis of molecular…

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…

RADami
Desktop

RADami

A partitioned restriction-site associated DNA (RAD) visualization method to…

A partitioned restriction-site associated DNA (RAD) visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate…

STS
Desktop

STS Sequential Tree Sampler

Implements several different transition kernels for updating a phylogenetic…

Implements several different transition kernels for updating a phylogenetic posterior with new sequences. STS is an open source package that updates an other distribution generated by MrBayes with…

FastNet
Desktop

FastNet

Infers phylogenetic networks from large-scale genomic sequence datasets.…

Infers phylogenetic networks from large-scale genomic sequence datasets. FastNet is based on a divide-and-conquer algorithm which permits to constrain the number of taxa and the evolutionary…

IsoSel
Desktop

IsoSel Isoform Selector

Selects alternative isoforms in the context of phylogenetic reconstruction.…

Selects alternative isoforms in the context of phylogenetic reconstruction. IsoSel is based on the SP score and allows to obtain datasets that are optimized for tree reconstruction. It is based on…

GEIGER
Desktop

GEIGER

Describes evolutionary radiations. GEIGER can carry out simulations, parameter…

Describes evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Its main purpose is to detect and describe evolutionary radiations.…

nextflu
Web

nextflu

A processing pipeline and browser-based visualization that allows convenient…

A processing pipeline and browser-based visualization that allows convenient exploration and analysis of the most recent influenza virus sequence data. nextflu displays a phylogenetic tree that can…

andi
Desktop

andi

A program for estimating the evolutionary distance between closely related…

A program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute…

ExaML
Desktop

ExaML Exascale Maximum Likelihood

A dedicated production-level code for inferring phylogenies on…

A dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers. ExaML addresses and provides generally applicable solutions for…

MulRF
Desktop

MulRF

A platform-independent software package for phylogenetic analysis using…

A platform-independent software package for phylogenetic analysis using multi-copy gene trees. It seeks the species tree that minimizes the Robinson-Foulds (RF) distance to the input trees using a…

MEvoLib
Desktop

MEvoLib

A molecular evolution library freely available for Python. MEvoLib offers a…

A molecular evolution library freely available for Python. MEvoLib offers a wide range of modules and methods that cover all the main stages involved in usual molecular evolution workflows. It…

πBUSS
Desktop

πBUSS

Generates large sequence alignments under complex evolutionary models. πBUSS…

Generates large sequence alignments under complex evolutionary models. πBUSS employs the BEAGLE high performance library for phylogenetic computations to facilitate the evaluation of estimator…

Phyldog
Desktop

Phyldog

A program made to simultaneously build gene and species trees when gene…

A program made to simultaneously build gene and species trees when gene families have undergone duplications and losses. It can analyze thousands of gene families in dozens of genomes simultaneously,…

GARLI
Desktop

GARLI Genetic Algorithm for Rapid Likelihood Inference

Performs phylogenetic searches on aligned nucleotide, codon and amino acid data…

Performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion.

GSI
Web
Desktop

GSI Genealogical Sorting Index

Quantifies the historical relationships among groups for any genealogy to…

Quantifies the historical relationships among groups for any genealogy to enable novel insight into the evolutionary process. GSI calculates the genealogical sorting index and measures its…

BMGE
Desktop

BMGE Block Mapping and Gathering with Entropy

Selects regions in a multiple sequence alignment that are suited for…

Selects regions in a multiple sequence alignment that are suited for phylogenetic inference. BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid…

ExPASy
Dataset

ExPASy Expert Protein Analysis System

Provides a comprehensive list of resources in different domains, such as…

Provides a comprehensive list of resources in different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics and transcriptomics. ExPASy is the Swiss…

CVTree
Web

CVTree

An implementation of the whole genome-based, alignment-free composition vector…

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…

STRAW
Web

STRAW Species TRee Analysis Web server

A web server that offers workflows for reconstruction of phylogenies of species…

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…

StarBEAST2
Desktop

StarBEAST2

Enables fuller use of available data and more accurate inference of species…

Enables fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates. StarBEAST2 is a more powerful and robust estimator of rate…

ChromoSSE
Desktop

ChromoSSE Chromosome State change Speciation and Extinction

A class of models of chromosome number evolution that incorporate both…

A class of models of chromosome number evolution that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allows to determine the mode of chromosome number evolution. These…

Accelerated Sim
Desktop

Accelerated Sim

Accelerates simulation of evolutionary trajectories in origin-fixation models.…

Accelerates simulation of evolutionary trajectories in origin-fixation models. Accelerated_Sim algorithm requires on average only about two fitness evaluations per fixed mutation, whereas traditional…

PolytomySolverN…
Desktop

PolytomySolverNAD

Is dedicated to the polytomy refinement problem. PolytomySolverNAD corrects a…

Is dedicated to the polytomy refinement problem. PolytomySolverNAD corrects a NAD (Non-Apparent Duplication) of the gene tree by applying multifurcation, given a rooted binary gene tree and species…

PhyloBayes
Desktop

PhyloBayes

A Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic…

A Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction.

BPhyOG
Web

BPhyOG Bacterial Phylogenies based on Overlapping Genes

Reconstructs the phylogenies of completely sequenced bacterial genomes based on…

Reconstructs the phylogenies of completely sequenced bacterial genomes based on overlapping genes. BPhyOG comprises three sections: (i) phylogenetic inference, which is mainly used to reconstruct…

leBIBI(QBPP)
Web

leBIBI(QBPP)

A powerful tool helping biologists to position bacterial or archaeal sequence…

A powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. leBIBI(QBPP) is a diagnostic tool for clinical, industrial and environmental…

BrassiBase
Dataset

BrassiBase

An online database system of cross-referenced information and resources on…

An online database system of cross-referenced information and resources on Brassicaceae taxonomy, systematics, evolution, traits and germplasm resources. Biological material and resources, either…

MacClade
Desktop

MacClade

Permits interactive analysis of character evolution and phylogeny. MacClade…

Permits interactive analysis of character evolution and phylogeny. MacClade displays a given tree and a matrix of character data reconstruction of character evolution by shading the branches of the…

POY
Desktop

POY

Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene…

Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is a phylogenetic analysis program that can perform true sequence…

BayesPhylogenie…
Desktop

BayesPhylogenies

Infers phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or…

Infers phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. BayesPhylogenies allows a range of models of gene sequence…

ASILA
Desktop

ASILA

Gets M (number of different haplotypes) and N (Number of SNP) as an input and…

Gets M (number of different haplotypes) and N (Number of SNP) as an input and generates all perfect phylogeny matrices with M different rows and N columns.

Fasturec
Desktop

Fasturec

A software for the inference of an optimal species tree under duplication and…

A software for the inference of an optimal species tree under duplication and duplication-loss cost from a set of unrooted gene trees. Fasturec determines an optimal species tree from collections of…

TreePar
Desktop

TreePar

Estimating birth and death rates based on phylogenies. TreePar, for a given…

Estimating birth and death rates based on phylogenies. TreePar, for a given species phylogeny on present day data which is calibrated to calendar-time, provides a method for estimating maximum…

BPP
Desktop

BPP Bayesian Phylogenetics and Phylogeography

A Bayesian Markov chain Monte Carlo (MCMC) program for analyzing DNA sequence…

A Bayesian Markov chain Monte Carlo (MCMC) program for analyzing DNA sequence alignments under the multispecies coalescent model (MSC). BPP analyses may include estimation of population size…

Wombac
Desktop

Wombac Wombat Bacteria

Finds core genome single-nucleotide polymorphisms (SNPs) from samples and…

Finds core genome single-nucleotide polymorphisms (SNPs) from samples and produces an alignment of those SNPs which can be used to build a phylogenomic tree. Wombac can handle 100s of samples and…

BAMBE
Desktop

BAMBE Bayesian Analysis in Molecular Biology and Evolution

Allows Bayesian analysis of phylogenies. BAMBE provides several programs…

Allows Bayesian analysis of phylogenies. BAMBE provides several programs allowing to analyze aligned DNA or RNA sequence and also the sampled trees and parameter values.

Bosque
Desktop

Bosque

Manages the computational resources involved in typical phylogenetic analyses.…

Manages the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a desktop application which manages sequence datasets and alignments. It can align using…

Clearcut
Desktop

Clearcut

Remains a popular method for distance-based phylogenetic tree reconstruction.…

Remains a popular method for distance-based phylogenetic tree reconstruction. Clearcut computes pairwise distances by first determining the percent identity between all sequence pairs. It retains the…

TreeTime
Desktop

TreeTime

Provides routines for ancestral sequence reconstruction and the inference of…

Provides routines for ancestral sequence reconstruction and the inference of molecular-clock phylogenies. TreeTime is a Markov chain Monte Carlo (MCMC) framework for Bayesian phylogeny…

ProteinEvolver
Desktop

ProteinEvolver

Simulates protein evolution. Protein Evolver combines models of protein folding…

Simulates protein evolution. Protein Evolver combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and…

PhyloPro
Web

PhyloPro

Uses the 120 available eukaryotic genome sequences to visualize the…

Uses the 120 available eukaryotic genome sequences to visualize the evolutionary trajectories of user-defined subsets of model organism genes. Applied to pathways or complexes, PhyloPro allows the…

RAxML-Light
Desktop

RAxML-Light

A tool for large-scale phylogenetic inference on supercomputers under maximum…

A tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. RAxML-Light implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX)…

BUCKy
Desktop

BUCKy

A free program to combine molecular data from multiple loci. BUCKy estimates…

A free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian…

STEM-hy
Desktop

STEM-hy Species Tree Estimation using Maximum likelihood

A software package written in the C language to obtain maximum likelihood (ML)…

A software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to…

TOPALi
Desktop

TOPALi

Simplifies and automates the use of several methods for the evolutionary…

Simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments.

HyPhy
Desktop

HyPhy Hypothesis testing using Phylogenies

An open-source software package for the analysis of genetic sequences using…

An open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.

TNT
Desktop

TNT Tree analysis using New Technology

It is a program for phylogenetic analysis under parsimony, as well as extensive…

It is a program for phylogenetic analysis under parsimony, as well as extensive tree handling and diagnosis capabilities.

SCI-PHY
Desktop

SCI-PHY Subfamily Classification In PHYlogenomics

A pipeline for automatic subfamily identification, followed by subfamily hidden…

A pipeline for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs…

ERATE
Desktop

ERATE

Treats insertions and deletions as evolutionary events. ERATE is an extension…

Treats insertions and deletions as evolutionary events. ERATE is an extension of DNAML program. It is applied to phylogenetic tree inference. Using standard benchmarking methods on simulated data and…

FlowerPower
Web
Desktop

FlowerPower

A package for the identification of global homologs as a precursor to…

A package for the identification of global homologs as a precursor to structural phylogenomic analysis. FlowerPower employs an iterative approach to clustering sequences. This tool identifies…

MP-EST
Desktop
Web

MP-EST Maximum Pseudo-likelihood for Estimating Species Trees

It can consistently estimate the topology and branch lengths (in coalescent…

It can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or…

Armadillo
Desktop

Armadillo

A workflow platform dedicated to phylogenetic as well as general bioinformatics…

A workflow platform dedicated to phylogenetic as well as general bioinformatics analysis.

mtDIS
Desktop

mtDIS

Implements a distance measure appropriate for single-copy DNA. mtDIS takes into…

Implements a distance measure appropriate for single-copy DNA. mtDIS takes into account the actual sequence divergence as well as frequency composition of the DNA haplotypes in the populations being…

STINGRAY
Web
Desktop

STINGRAY System for Integrate Genomic Resources and Analyses

Offers a complete annotation pipeline for integrating, analyzing, annotating…

Offers a complete annotation pipeline for integrating, analyzing, annotating and presenting genomic and expression data from sequencing platforms. STINGRAY offers to user a phylogenetic module that…

TreSpEx
Desktop

TreSpEx Tree Space Explorer

Combines different approaches (including statistical tests), which utilize…

Combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. TreSpEx enables the…

iGTP
Desktop

iGTP

A program designed to help biologists infer species phylogenies from gene…

A program designed to help biologists infer species phylogenies from gene phylogenies, using the gene tree parsimony (GTP) approach. The program implements efficient heuristics which allows it to…

PhyloNet
Desktop

PhyloNet Phylogenetic Networks Toolkit

Offers an array of utilities to allow for efficient and accurate analysis of…

Offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying…

Fastphylo
Desktop

Fastphylo

A software package containing implementations of efficient algorithms for two…

A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a…

FLK
Desktop

FLK

Serves to detect selection in population trees, in particular the Lewontin and…

Serves to detect selection in population trees, in particular the Lewontin and Krakauer test extended. FLK allows to compare patterns of difference between allele frequencies according to several…

DistMiss
Desktop

DistMiss

Calculates a matrix of genetic distances populations based of their allele…

Calculates a matrix of genetic distances populations based of their allele frequencies at L loci. The DistMiss calculation is available in the PHYLIP software as well as in many population genetics…

RDP Tree…
Web

RDP Tree Builder

Allows to create a phylogenetic tree with bootstrap confidence estimates using…

Allows to create a phylogenetic tree with bootstrap confidence estimates using the Weighbor Joining method. RDP Tree Builder is a method that uses a Java applet for displaying and saving tree. It…

nextstrain
Dataset

nextstrain

Provides a real-time snapshot of evolving viral populations and interactive…

Provides a real-time snapshot of evolving viral populations and interactive data visualizations. Nextstrain aims to allows virologists, epidemiologists, public health officials and citizen scientists…

fastDNAml
Desktop

fastDNAml