91 Free Phylogenetics Tools - Software and Resources

Phylogenetic inference and data visualization.

PSMC (Pairwise Sequentially Markovian Coalescent) is a tool for inferring population history from whole-genome sequence data.

node.dating is a software tool for the divergence-time analysis to estimate the dates of the internal nodes of phylogenetic trees. The node.dating algorithm uses a maximum-likelihood method to estimate the dates of the internal nodes of phylogenetic trees.

MSMC (Multiple Sequentially Markovian Coalescent) is a software tool for analyzing and estimating the history of separation among populations. The MSMC algorithm can identify complicated demographic scenarios implicating post-split admixture or archaic introgression.

EmpPrior is a software tool to estimate branch-length priors for phylogenetics. EmpPrior queries the TreeBASE database to find data similar to taxonomic and genetic sampling at hand and utilizes them to report branch-length priors for further analysis. The EmpPrior consists of EmpPrior-search for querying TreeBASE and EmpPrior-fit for parameterizing branch-length distributions.

MEGA (Molecular Evolutionary Genetics Analysis) is a software tool package for analyzing and visualizing molecular evolution. The MEGA package includes a large variety of analysis methods, such as editing of aligned sequence data, construction of time trees, divergence estimation, computation of confidence intervals to calibrate parameters for node-dating tip-dating, and Bayesian method to estimate evolutionary probabilities and more.

PHYLIP is a comprehensive software tool package for phylogenetic analyses. The PHYLIP package includes tools to infer evolutionary trees (phylogenies), parsimony, distance matrix, likelihood, bootstrapping, consensus trees, and discrete characters. The algorithm includes heuristic, branch, and bound tree search.

GENLIB is an R tool for the analysis of genealogical data. The functions include extracting and selecting portions of data and individuals, descriptive statistics, inbreeding, kinship, and genetic contribution computations.

Polyunphased extends the Unphased package by adding polytomous phenotypes.

PhySortR is an R package to screen and sort phylogenetic trees.

ProteinHistorian is a tool for the identification of protein enrichment by phylogenetic age.

Dendroscope is a software tool to compare rooted phylogenetic networks. The Dendroscope has algorithms for comparison, computing, and visualizing phylogenetic and hybrid networks and trees.

UFBoot (ultrafast bootstrap approximation) is a software tool for bootstrapping phylogenetic trees and phylogenetic data resampling. UFBoot is in the IQ-TREE package.

SigTree is an R tool package that contains a collection of functions for identifying and visualizing phylogenetic tree branches that show effective responses for operational taxonomic unit abundance in a microbial community. The SigTree functions take as inputs a phylogenetic tree of class phylo and corresponding tip (OTU) labels and p-values.

bModelTest is a software tool to test, compare, infer, and marginalize phylogenetic models for BEAST 2. The bModelTest algorithm uses trans-dimensional Markov chain Monte Carlo (MCMC).

ALFRED-G is a bioinformatics software tool to estimate evolutionary distances between two sequences. The ALFRED-G algorithm uses a greedy alignment-free method.

BEAST 2 is a bioinformatics software package for Bayesian evolutionary analyses of molecular sequences, reconstructing phylogenies, and testing evolutionary hypotheses. The BEAST 2 algorithm uses Markov chain Monte Carlo (MCMC). A variety of additional user-installable tools/packages is available.

RevBayes is a software package for statistical computation, modeling, and simulation of Bayesian inference in phylogenetics. The RevBayes has an interactive environment and uses interpreted 'Rev' scripting language specific to RevBayes.

apex is an R tool for use in phylogenetics to handle, analyze, store, and visualize DNA and amino acid sequence data.

SILVA Tree Viewer is a web-based tool to visualize large phylogenetic trees. The SILVA interface uses Web Geographic Information Systems (Web-GIS) Recourse and a PostgreSQL database.

LNJ is a software tool to construct phylogenetic trees using heuristics. The LNJ algorithm extends Neighbor-Joining (NJ) by including options to use NJ or permitting a live internal node in cases where the creation of a live internal node produces a smaller branch number than NJ.

DAMBE7 is a tool for genomic and phylogenetic sequence data analysis. The DAMBE7 package includes functions for 1. Sequence alignment, 2. Molecular phylogenetics, 3. Position weight matrix to analyze sequence motifs, 4. Perceptron for classification of sequence motifs, 5. Gibbs sampler, 6. Hidden Markov models, 7. Secondary structure prediction, 8. rRNA anticodon identification, 9. Codon usage bias, 10. Computation of isoelectric point, and 11. Peptide mass fingerprinting. DAMBE7 works with a variety of well-known sequence formats.

phylotree.js is a JavaScript library to visualize interactively phylogenetic data and develop applications. The phylotree.js library extends D3.js hierarchy and includes functions for scaling, animated re-rooting of threes, ladderization, collapsing/hiding large trees, node, clade, and subtree selection, conditional selection of tree branches, customization of style.

treeman is an R library to represent and manipulate phylogenetic trees in various ways.

VCFtoTree is a user-friendly software tool that allows researchers to easily construct sequence alignments and phylogenetic trees for specific genomic regions using data from large-scale genome sequencing projects. The tool integrates thousands of anthropologically relevant genomes, including those from the 1000 Genomes Project, Neanderthal and Denisovan genomes, and reference genomes of chimpanzees and rhesus macaques.

The software directly accesses online databases to download and parse genome variation data for the regions of interest. It combines popular sequence datasets and tree-building algorithms with custom data parsing to generate accurate alignments and phylogenies. VCFtoTree can also be applied to other phased human genomes and genomes from other species.

The tool provides a graphical user interface, making it accessible to a wider audience without requiring programming knowledge.

Treeio is a software package that addresses the issue of incompatible and inconsistent formats in phylogenetic trees and data. It enables the extraction and integration of phylogenetic trees and outputs from various analytical software tools, allowing for comparative studies and merging tree data from different sources. Treeio also facilitates linking external data to phylogenies, enabling analyses of phylogeny-associated data from various disciplines in an evolutionary context.

The package supports the export of phylogenetic trees with heterogeneous-associated data to a single tree file, including BEAST-compatible NEXUS and jtree formats, promoting data sharing and file format conversion for downstream analysis. Treeio is designed to work seamlessly with the tidytree and ggtree packages, enabling tree data processing using the tidy interface and visualization through ggtree.

Spectre is an R package designed to provide a comprehensive and scalable approach to analyzing high-dimensional cytometry data. It allows for the integration and analysis of data from multiple batches or experiments, including flow cytometry, mass cytometry (CyTOF), spectral cytometry, single-cell RNA sequencing (scRNAseq), and high-dimensional imaging technologies like Imaging Mass Cytometry (IMC). The package includes features for raw data pre-processing, batch alignment, data integration, clustering, dimensionality reduction, visualization, and population labeling, as well as quantitative and statistical analysis. Its modular design makes it accessible to both bioinformaticians and laboratory scientists. Spectre is available as an R package or Docker container, with R code available on GitHub at .

castor is an R tool to manipulate large phylogenetic trees. The castor algorithm includes functions to prune, reroot, compute pairwise distances and from the tree's root, compute phylogenetic signal statistics, construct ancestral traits, and predict hidden characters.

PhyloMAd is a software tool for the assessment of phylogenomic model adequateness. The PhyloMAd algorithm uses IQ-TREE for Maximum Likelihood inference, parametric bootstrap simulations and various standard statistical tests. The package includes functions assessing substitution saturation by measuring entropy, phylogenetic tree topology signal strengths, and accuracy of number and clock mode

PhyloProfile is a software tool to visualize using R Shiny and investigate multi-layered phylogenetic profiles. The PhyloProfile package can display presence and absence patterns of orthologs, sequence similarity, and domain architecture among orthologs, dynamic filtering of profiles, and estimate the age of genes and differences in functional annotations. The PhyloProfile uses NCBI taxonomy to collapse systematics groups.

EvolView is a web-based resource to visualize, annotate, and handle phylogenetic trees. EvolView allows visualization of trees as circular or rectangular phylograms, cladograms And several styling options. The EvolView functions include many annotation variants, pie and bar charts, heatmap, dot plot, and more.

IcyTree is a web-based tool to visualize phylogenetic trees and networks using various visualization styles. IcyTree also includes lineages-through-time and Skyline plots.

phylodyn is an R tool package to estimate effective population size fluctuations over time using nonparametric Bayesian. The phylodyn algorithm uses the Markov chain Monte Carlo (MCMC) method and integrated nested Laplace (INLA) approximation for phylodynamic inference.

PhyloNet (Phylogenetic Regulatory Network) is a tool package to analyze and reconstruct phylogenetic networks and evolutionary relationships from data sets of unlinked loci. The PhyloNet algorithms include Maximum Parsimony, likelihood, and Bayesian inference functions.

W-IQ-TREE is a web-based tool for phylogenetic Maximum Likelihood analysis using DNA, protein, binary, morphology, and codon data. The W-IQ-TREE algorithm includes functions for various evolutionary models. See also IQ-TREE package.

ASTRAL is a tool to estimate unrooted species trees from sets of unrooted trees. The ASTRAl algorithm uses a multi-species coalescent model and runs in polynomial time.

bdvis is a software package that provides functions to view various characteristics of biodiversity information in primary biodiversity records (PBRs). The bdvis includes taxonomic and temporal coverage functions, geographic biases, and the completeness of the inventory.

A web interface at Expasy for ClustalW multiple sequence alignment (MSA) tool. Works with both nucleic acid and protein sequences.

A web-based implementation at BCP - CNRS Université Lyon of Clustal W multiple sequence alignment software for protein and DNA sequences.

Newick Utilities is a software tool package to manipulate phylogenetic trees. The Newick Utilities package includes trim, re-root, condense, and draw functions.

DIALIGN-TX is the latest version of the DIALIGN multiple sequence alignment (MSA) tool. The main algorithmic addition is the usage of a guide tree.

A web-based application, which utilizes CHAOS database search tool to find a list of local sequence similarities. DIALIGN uses these similarities as anchor points to construct multiple sequence alignments.

PAML is a tool package for reconstructing and fitting models of phylogenetic trees. The PAML algorithm uses the Maximum Likelihood (ML) method.

FastTree is a software tool for constructing phylogenetic trees using approximately maximum likelihood. The FastTree algorithm uses nearest-neighbor interchanges (NNIs), minimum-evolution criterion, minimum-evolution subtree-pruning-regrafting (SPRs), maximum-likelihood NNIs, heuristics, and rate of evolution estimation.

TESS is an R tool to estimate diversification rates and simulate reconstructed phylogenetic trees using tree-wide time-heterogeneous birth/death processes that include mass extinction events. The TESS algorithm includes functions for Maximum Likelihood (ML) estimation and Bayesian inference of rates for lineage diversification.

DIALIGN is a multiple sequence alignment (MSA) tool. An improved version is called DIALIGN-TX which in turn is an improvement over DIALIGN-T, that combines greedy, progressive methods. See also 'LINKS'.

There are two versions of Clustal 2 multiple sequence alignment software: 1) Clustal W command-line tool and 2) Clustal X with graphical user interface.

Phylo.io is a web-based tool to interactive viewing and comparing phylogenetic trees side by side.

jsPhyloSVG is a tool to render using the phylogenetic XML schema phyloXML. jsPhyloSVG permits customization of the trees and can render complicated trees.

BARCOD makes a character matrix using Véronique Barriel’s method, coding each insertion/deletion event regardless of the length into a single event and retains common indels.

GEIGER is an R tool to analyze, simulate, and estimate parameters for evolutionary radiations. The GEIGER algorithm includes functions for statistical hypothesis testing and analyzing the statistical power. Among others, the GEIGER package includes the following published methods: Time-scaling large phylogenies with 'congruification,' identifying shifts in the rate of diversification, identifying shifts in the rate of diversification, using fossil information to improve macroevolutionary inference, fitting discrete models of evolution, fit continuous trait models to unresolved data using ABC, identify shifts in the rate of continuous trait evolution, fit continuous models of evolution, and fit discrete models of evolution.

edialign is an EMBOSS version of DIALIGN 2 multiple sequence alignment (MSA) tool.

iTOL, Interactive Tree Of Life, is a web-based tool to display and annotate phylogenetic trees. The free access allows users to create unlimited workspaces and projects, upload trees, use annotation functions that cannot be saved but can be exported, and use the batch upload function.

LNETWORK is a software tool for constructing phylogenetic networks from an input of a set of rooted phylogenetic trees.

T-Coffee is a multiple sequence alignment (MSA) program. Web user interface and web services interfaces at EBI provides Simple Object Access Protocol (SOAP), Representational State Transfer (REST), Open API Interface, and Common Workflow Language (CWL) services. T-Coffee package pre-processes the data by making pair-wise alignments between all sequences and this information is incorporated in the progressive alignment procedure. The structural sequence information may be obtained from various different sources. It can align amino acid and nucleotide sequences. The package combines several alignment methods.

TriLoNet (Trinet Level-one Network) is a software tool that constructs rooted level-1 phylogenetic networks from DNA sequence alignments to Reconstruct Reticulate Evolutionary Histories. The TriLoNet algorithm assembles small phylogenetic networks using a bottom-up approach similar to Neighbor-Joining.

webPRANK is a multiple sequence alignment (MSA) tool for DNA, protein, cDNA, and codon sequences at Goldman Group (EBI). It has structure models built-in and includes a web-based visualization of multiple alignments.

STELLS is a tool to infer species trees from gene tree topologies. The STELLS algorithm uses coalescent-based maximum likelihood and includes functions for inference with haplotypes and to compute the Gene Tree Probability with the Multispecies Coalescent.

IQ-TREE is a software package for phylogenetic inference, including tree reconstruction, model selection, bootstrap approximation (UFBoot), and big data analysis. The IQ-TREE algorithm includes various evolutionary models, such as mixture, partition, and common substitution.

HmmCleaner is a tool to remove alignment and sequencing error containing segments from multiple sequence alignments (MSA) using profile hidden Markov models (pHMM). This tool is based on Bio::MUST modules and integrates into MUST environment.

A web-based tool for multiple sequence alignment (MSA) of DNA. The algorithm uses PFAM or profiles provided by a user. The web interface requires registration and login.

The multiple sequence alignment (MSA) tool, CUDA ClustalW v1.0 is a GPU version of ClustalW v2.0.1, using synchronous diagonal multiple threads and internal tasks' parallelization. The Authors report it to be able to speed up about 22 times compared to running on a single CPU.

HAlign-II is a tool for multiple sequence alignment of amino acid and nucleotide sequences and phylogenetic tree construction aimed for sequence files bigger than one Gb. The software can be used in standalone or in Hadoop cluster mode. HAlign-II contains three types of sequence alignment methods and a large-scale phylogenetic tree construction method based on Apache Spark platform. You can also run HAlign-II on the web server on the clusters in Tianjin University (Spark & Hadoop cluster and NVIDIA K80 GPU cluster). The webserver is accessible from the HAlign-II web pagepage.

FAMSA is designed to produce rapid multiple sequence alignment of large protein families. It first determines the longest common subsequences and has a unique way to compute gap costs. It proceeds progressively to add sequences into the alignments using a novel iterative approach. The Authors claim FAMSA to be superior to Clustal Omega and MAFFT. A GPU version is available.

KMAD is a software package specifically designed to construct multiple sequence alignments (MSAs) of so-called intrinsically disordered proteins (IDPs). IDPs differ from globular proteins by lacking tertiary structure and by having lower sequence conservation. The Authors provide both stand-alone and web server versions.

VerAlign is a web-based tool to compare two multiple sequence alignments (MSAs). It uses SPdist scoring scheme which measures a distance between mismatched amino acid pairs. Available from the Authors upon request.

MSARC a multiple sequence alignment (MSA) tool that constructs alignments without guide trees. The Authors claim their method to outperform BAliBASE on "sequence sets whose evolutionary distances are difficult to represent by a phylogenetic tree."

A tool for improving multiple sequence alignments using probabilistic sampling.

EDNA (Energy Based Multiple Sequence Alignment) is a multiple sequence alignment (MSA) program for aligning transcription factor binding site sequences (TFBSs). The novelty of this software is the scoring using a thermodynamically generated null hypothesis. The method is well suited for aligning sequences that are often not related. Alternative names: Energy Based Multiple Sequence Alignment, EDNA

MSACompro is a tool to integrate tool predicted secondary structure, residue contact information, and relative solvent accessibility into a posterior probability for multiple sequence alignment (MSA) software, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT, and MUSCLE.

Enhanced multiple sequence alignment (MSA) software at Brigham Young University, Computer Science Department. This software uses hardware acceleration: GPU, FPGA, and Cell BE.

A command-line-based tool for computation of guide trees for multiple sequence alignments (MSAs).

A parallelized version of MAFFT multiple sequence alignment (MSA) tool. The parallelization is based on the POSIX Threads library with two approaches: best-first and simple hill-climbing in the alignment refinement stage.

Probalign is a multiple sequence alignment (MSA) software that uses a partition function to estimate posterior alignment probabilities. The Authors claim Probalign to be more accurate than Probcons, MAFFT, and MUSCLE.

BAliBASE (Benchmark Alignment dataBASE) is a multiple sequence alignment (MSA) benchmarking reference set. It contains reference alignments based on three-dimensional structures and particular reference sets that contain various linear motifs. The AUthors also provide a program that can compare a test alignment with the BAliBASE reference alignment.

EMBL-Align is a publicly available database of multiple sequence alignments (MSAs). An associated tool, Webin-Align is a tool for submission of alignments. the EBI SRS (Sequence Retrieval System) server is used to query all the multiple sequence alignments.

DIALIGN 2 is an improved version of the original multiple sequence alignment tool DIALIGN from the year 1997. This tool uses sequence segments that don't contain indels for alignment construction. The most recent version of DIAGLIGN is called DIALIGN-TX. See the 'LINKS'.

A version of the Clustal 2 multiple sequence alignment program with a graphical interface.

T-Coffee is a multiple sequence alignment (MSA) program. It preprocesses the data by making pair-wise alignments between all sequences and this information is incorporated in the progressive alignment procedure. The structural sequence information may be obtained from various different sources. It can align amino acid and nucleotide sequences.

M-Coffee is a particular mode of T-Coffee software.

PSI-Coffee is a part of the T-Coffe distribution and specifically designed for making multiple sequence alignments (MSAs) of alpha-helical transmembrane protein sequences. The Authors claim PSI-Coffee to be more accurate than MSAProbs, Kalign, PROMALS, MAFFT, ProbCons, and PRALINE.

BAliBASE (Benchmark Alignment dataBASE) is a multiple sequence alignment (MSA) benchmarking reference set. It contains reference alignments based on three-dimensional structures and particular reference sets that contain various linear motifs. The AUthors also provide a program that can compare a test alignment with the BAliBASE reference alignment. See also "links" for BAliBASE.

ClonArch is a software tool for visualizing the spatial distribution of clones and phylogenetic trees. The ClonArch algorithm uses marching squares to compute perimeters between actual and simulated tumor clones.

P3 is an add-on to the RevBayes software package, providing tests of model fit that uses posterior predictive and inference-based tests.

Phylostat is a web-based tool to visualize, statistically compare, and analyze clade divergence of phylogenetic trees.

pplacer is a tool for phylogenetic placement, a version of phylogenetic tree construction, and visualization.

Fastbaps is a rapid and efficient solution to the genetic clustering challenge, particularly tailored for multilocus genotype data. This software implements an approximate fit to a Dirichlet process mixture model (DPM), enabling it to handle substantially larger datasets—ranging from 10 to 100 times—than those manageable by existing model-based clustering methods. A key demonstration of its capability is the analysis of an alignment comprising over 110,000 sequences of HIV-1 pol genes, showcasing its robustness and scalability.

Beyond mere clustering, Fastbaps offers a novel approach for partitioning existing hierarchies to maximize the DPM model's marginal likelihood. This feature allows for the splitting of phylogenetic trees into clades and subclades based on a population genomic model, offering a nuanced view of genetic relationships and variations.

TREEasy is a workflow tool to deduce gene and species trees and phylogenetic networks using multilocus data. The TREEasy workflow uses MAFFT, IQ-Tree, RaxML-NG, ASTRAL, MP-EST, STELLS2, SNaQ, and PhyloNet tools.

RaxML-NG is a tool to infer phylogenetic trees. The RaxML-NG uses Maximum Likelihood (ML) and has functions for transfer bootstrap support metrics and detecting terraces within tree space.

MP-EST is a software tool for estimating a species tree from a set of rooted binary gene trees. The MP-EST algorithm uses the pseudo-likelihood method and has functions to collapse short internal branches, compute triple frequencies of gene trees, and output a set of triples decomposed from each tree.

SNaQ is a tool package to infer, manipulate, visualize, and interactively use phylogenetic networks. The SNaQ algorithm employs Maximum Pseudolikelihood (ML) method and bootstrap analysis and incorporates functions for summarising a set of networks.