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 inference is considered a hard…
PhyloPat PhyloPat

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…

Desktop app
FastTree FastTree

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)…

Desktop app
sampled-ancestors sampled-ancestors

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…

Desktop app
TreeExp TreeExp

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…

Desktop app
DiscoMark DiscoMark

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…

Desktop app
Phylo-Node Phylo-Node

Phylo-Node

A scalable toolkit that allows the user to go from sequence retrieval to…

A scalable toolkit that 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…

Desktop app
TransPhylo TransPhylo

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…

Desktop app
Phylogenetic… Phylogenetic Likelihood Library

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…

Desktop app
Phycas Phycas

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…

Web app
Bacterial Phylogenies… Bacterial Phylogenies based on Overlapping Genes

BPhyOG Bacterial Phylogenies based on Overlapping Genes

A web app to reconstruct the phylogenies of completely sequenced bacterial…

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

Desktop app
Genome Topology… Genome Topology Network

GNT Genome Topology Network

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

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

Desktop app
AutoMated… AutoMated PHylogenomic infeRence Application

AMPHORA2 AutoMated PHylogenomic infeRence Application

An automated pipeline for phylogenomic analysis that overcomes the existing…

An automated pipeline for phylogenomic analysis that overcomes the existing bottlenecks limiting large-scale protein phylogenetic inference. Up to 20.000 bacterial protein markers are used by…

Desktop app
Phyla-AMPHORA Phyla-AMPHORA

Phyla-AMPHORA

Performs large-scale phylogenetic inference using phylum-specific bacterial…

Performs large-scale phylogenetic inference using phylum-specific bacterial phylogenetic markers. A database was created by surveying all complete bacterial genomes and identifying single-copy genes…

Desktop app
ASILA ASILA

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.

Desktop app
PhyloGenie PhyloGenie

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…

Desktop app
Phylogenetic analyses… Phylogenetic analyses using Deep Mutational…

phydms Phylogenetic analyses using Deep Mutational Scanning

This package uses a null model based on high-throughput measurements of a…

This package uses a null model based on high-throughput measurements of a gene’s site-specific amino-acid preferences to detect sites of positive selection. phydms can use Experimentally Informed…

Desktop app
R PHylogenetic… R PHylogenetic Analysis with Space/Time models

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…

Desktop app
Fasturec Fasturec

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…

Desktop app
Tree Independent… Tree Independent Generation of Evolutionary Rates

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…

Desktop app
TreeSimGM TreeSimGM

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,…

Desktop app
TreeSim TreeSim

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…

Desktop app
TreePar TreePar

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…

Web app
Desktop app
Genealogical Sorting… Genealogical Sorting Index

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…

Desktop app
RevBayes RevBayes

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…

Desktop app
PyRate PyRate

PyRate

A python program to estimate speciation, extinction, and preservation rates…

A python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. Pyrate includes several methods to understand how rates vary…

Desktop app
MultiTypeTree MultiTypeTree

MultiTypeTree

A package capable of sampling from posterior distributions over structured…

A package capable 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…

Web app
Desktop app
POPTREEW POPTREEW

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…

Desktop app
πBUSS πBUSS

πBUSS

A simulation tool to generate large sequence alignments under complex…

A simulation tool to generate large sequence alignments under complex evolutionary models. πBUSS employs the BEAGLE high performance library for phylogenetic computations to facilitate the…

Desktop app
Block Mapping and… Block Mapping and Gathering with Entropy

BMGE Block Mapping and Gathering with Entropy

A package to select regions in a multiple sequence alignment that are suited…

A package to select 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…

Desktop app
RADami RADami

RADami

A partitioned RAD visualization method to investigate the possibility that…

A partitioned RAD visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage…

Web app
Desktop app
IQ-TREE/W-IQ-TREE IQ-TREE/W-IQ-TREE

IQ-TREE/W-IQ-TREE

An efficient and versatile phylogenetic software for maximum likelihood…

An efficient and versatile phylogenetic software for maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than…

Desktop app
sampletrees/Rsampletrees

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…

Desktop app
Evolutionary Rates… Evolutionary Rates and Branch Length Estimation

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…

Desktop app
ExaBayes ExaBayes

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…

Desktop app
the PHYLogeny… the PHYLogeny Inference Package

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…

Desktop app
TreeTime TreeTime

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…

Desktop app
phyloSkeleton phyloSkeleton

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,…

Web app
Desktop app
System for Integrate… System for Integrate Genomic Resources and…

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…

Desktop app
HOGAN HOGAN

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…

Desktop app
Genealogies Unbiased… Genealogies Unbiased By recomBinations In…

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…

Desktop app
ChromEvol ChromEvol

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…

Desktop app
Chromosome State… Chromosome State change Speciation and Extinction

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…

Desktop app
Accelerated Sim Accelerated Sim

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…

Desktop app
bayesian Model Test bayesian Model Test

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…

Desktop app
MEvoLib MEvoLib

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…

Desktop app
CloudPhylo CloudPhylo

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…

Desktop app
Phylogenetics,… Phylogenetics, Evolutionary Biology, and…
Desktop app
Treemaker Treemaker

Treemaker

Allows the interactive building and editing of a taxonomy and its conversion…

Allows the interactive building and editing of a taxonomy and its conversion into a phylogeny for the above calculations. It also allows the editing of site abundance and species richness data. This…

Desktop app
Immunopeptidome-based… Immunopeptidome-based Tree of Life

iTree Immunopeptidome-based Tree of Life

A package to construct whole-genome or whole-proteome based phylogenetic trees…

A package to construct whole-genome or whole-proteome based phylogenetic trees without sequences alignment. iTree uses "Jaccard similarity coefficient" to calculate the evolution distances…

Desktop app
ProtEvol ProtEvol

ProtEvol

A package to generate independent site-specific amino acid distributions.…

A package to generate 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…

Desktop app
ProteinEvolver ProteinEvolver

ProteinEvolver

A package to simulate protein evolution. Protein Evolver combines models of…

A package to simulate 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…

Web app
RaPPer RaPPer

RaPPer

Generates random phylogeny matrix. RAPPER is based on a graph-theory approach…

Generates random phylogeny matrix. RAPPER is based on a graph-theory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n…

Desktop app
Subfamily… Subfamily Classification In PHYlogenomics

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…

Desktop app
Bayesian… Bayesian Phylogenetics and Phylogeography

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…

Desktop app
Wombat Bacteria Wombat Bacteria

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…

Desktop app
Mixture of Trees… Mixture of Trees using Expectation Maximization

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…

Desktop app
ERATE ERATE

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…

Desktop app
ghost-tree ghost-tree

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"…

Desktop app
TESS TESS

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…

Web app
leBIBI(QBPP) leBIBI(QBPP)

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…

Desktop app
andi andi

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…

Desktop app
Tree Space Explorer Tree Space Explorer

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…

Web app
PhyloPro PhyloPro

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…

Desktop app
RAxML-Light RAxML-Light

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)…

Desktop app
Exascale Maximum… Exascale Maximum Likelihood

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…

Desktop app
Phylogenies Updated… Phylogenies Updated PERperpetually

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…

Web app
CVTree CVTree

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…

Desktop app
Accurate Species TRee… Accurate Species TRee ALgorithm

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…

Desktop app
BUCKy BUCKy

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…

Desktop app
iGTP iGTP

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…

Desktop app
Web app
Maximum… Maximum Pseudo-likelihood for Estimating Species…

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…

Desktop app
Phyldog Phyldog

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,…

Web app
Species TRee Analysis… Species TRee Analysis Web server

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…

Desktop app
Species Tree… Species Tree Estimation using Maximum likelihood…

STEM-hy Species Tree Estimation using Maximum likelihood (with hybridization)

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…

Desktop app
MulRF MulRF

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…

Desktop app
Phylogenetic Networks… Phylogenetic Networks Toolkit

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…

Desktop app
Bio.Phylo Bio.Phylo

Bio.Phylo

A Python software library for working with phylogenetic data that is tightly…

A Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology.

Desktop app
PhyloTreePruner PhyloTreePruner

PhyloTreePruner

A utility that uses a phylogenetic approach to refine orthology inferences made…

A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.

Desktop app
Armadillo Armadillo

Armadillo

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

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

Desktop app
Bayesian Analysis in… Bayesian Analysis in Molecular Biology and…
Desktop app
Fastphylo Fastphylo

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…

Desktop app
Phylogenetic analysis… Phylogenetic analysis using parsimony*

PAUP* Phylogenetic analysis using parsimony*

It implements parsimony, distance and likelihood methods of phylogeny…

It implements parsimony, distance and likelihood methods of phylogeny reconstruction.

Desktop app
PhyML PhyML

PhyML

A phylogeny software based on the maximum-likelihood principle.

A phylogeny software based on the maximum-likelihood principle.

Desktop app
Reference sequence… Reference sequence Alignment-based Phylogeny…
Desktop app
TOPALi TOPALi

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.

Desktop app
Tree analysis using… Tree analysis using New Technology

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.

Desktop app
Bayesian Evolutionary… Bayesian Evolutionary Analysis by Sampling Trees

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…

Desktop app
Genetic Algorithm for… Genetic Algorithm for Rapid Likelihood Inference

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.

Desktop app
Hypothesis testing… Hypothesis testing using Phylogenies

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.

Desktop app
Molecular… Molecular Evolutionary Genetics Analysis

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…

Desktop app
MrBayes MrBayes

MrBayes

A program for Bayesian inference and model choice across a wide range of…

A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Desktop app
Phylogenetic Analysis… Phylogenetic Analysis by Maximum Likelihood

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…

Desktop app
Kdetrees Kdetrees

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.

Desktop app
Randomized Axelerated… Randomized Axelerated Maximum Likelihood

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.

Desktop app
PhyloBayes PhyloBayes

PhyloBayes

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

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

Desktop app
PHylogenetic Analysis… PHylogenetic Analysis with Space/Time models

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,…

Felsenstein’s… Felsenstein’s website

Felsenstein’s website

Phylogeny programs page describing all known software for inferring phylogenies…

Phylogeny programs page describing all known software for inferring phylogenies (evolutionary trees).

Desktop app
REfining Neighboring… REfining Neighboring Trees

RENT REfining Neighboring Trees

A heuristic method to infer local tree topologies with recombinant SNP…

A heuristic method to infer local tree topologies with recombinant SNP sequences in populations. The main idea of RENT is to jointly refine the set of local trees at given sites guided by several…

Desktop app
Rateevolver Deprecated Rateevolver

Rateevolver

Simulates the evolution of the substitution rate on a fixed nine-taxon tree.…

Simulates the evolution of the substitution rate on a fixed nine-taxon tree. RateEvolver can generate sequences under models of nucleotide substitution ranging from a Jukes-Cantor model to the HKY85…

Desktop app
Mac5 Deprecated Mac5

Mac5

Implements Bayesian estimation of phylogenetic trees from DNA multiple…

Implements Bayesian estimation of phylogenetic trees from DNA multiple alignments containing gaps. MAC5 uses Markov Chain Monte Carlo (MCMC) to sample from the posterior distribution of trees,…

Desktop app
DendroBLAST Deprecated DendroBLAST

DendroBLAST

A method for reconstructing phylogenetic dendrograms/trees from protein…

A method for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. DendroBLAST incorporates a simple model of sequence evolution to test the effect of introducing sequence…

Web app
Desktop app
FlowerPower Deprecated FlowerPower

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…

Curators for Phylogenetic inference

  • Abdoulaye Baniré Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…

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