Phylogenetic Pathways
A scholarly exploration of computational tools and methodologies for reconstructing the tree of life.
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What is Phylogenetics?
Reconstructing Evolutionary History
Phylogenetics is the study of evolutionary relationships among groups of organisms, often represented visually as a phylogenetic tree. These trees illustrate the inferred evolutionary history and relationships between species, genes, or other entities.
Computational Approaches
Computational phylogenetics leverages algorithms and software to infer these evolutionary relationships from biological data, typically DNA or protein sequences. This field is a cornerstone of modern bioinformatics, providing the tools necessary to analyze vast datasets and model complex evolutionary processes.
Diverse Applications
The software and methods within phylogenetics are broadly applied across various scientific disciplines, including comparative genomics, where researchers compare entire genomes to understand evolutionary divergence; cladistics, a method of classifying organisms based on shared derived characteristics; and general bioinformatics, which encompasses the development and application of computational tools to biological data.
Key Inference Methods
Distance Matrix Methods
These methods construct phylogenetic trees based on a matrix of pairwise distances between sequences. The distances represent the evolutionary divergence between each pair of sequences. Common algorithms include:
- Neighbor-Joining: A bottom-up (agglomerative) clustering method that iteratively finds pairs of operational taxonomic units (OTUs) that minimize the total branch length at each step.
- UPGMA (Unweighted Pair Group Method with Arithmetic Mean): A simpler clustering method that assumes a constant rate of evolution (molecular clock) and builds trees by grouping the closest pairs of sequences.
Maximum Parsimony
Maximum parsimony (often simply called parsimony) seeks the phylogenetic tree that requires the fewest evolutionary changes (e.g., nucleotide substitutions or character state changes) to explain the observed data. The principle is to find the simplest explanation for the observed character distribution.
Maximum Likelihood
Maximum likelihood methods infer the tree that maximizes the probability of observing the given sequence data, considering a specific model of evolution. This approach evaluates different tree topologies and branch lengths to find the one that best fits the data under the chosen evolutionary model.
Bayesian Inference
Bayesian phylogenetic inference uses Bayes' theorem to calculate the posterior probability of a tree, given the observed data and a prior probability distribution of trees and model parameters. It typically employs Markov Chain Monte Carlo (MCMC) methods to sample trees from the posterior distribution, providing a measure of confidence for each part of the inferred phylogeny.
Software Catalog
The following table compiles a selection of computational phylogenetics software, detailing their primary functions, the methods they employ, and their authors. This list highlights the diversity and specialization within the field, from general-purpose platforms to highly specific analytical tools.
| Name | Description | Methods | Author |
|---|---|---|---|
| ADMIXTOOLS | R software package that contains the qpGraph, qpAdm, qpWave, and qpDstat programs | Nick Patterson, David Reich | |
| AncesTree | An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data. | Maximum Likelihood, Integer Linear Programming (ILP) | M. El-Kebir, L. Oesper, H. Acheson-Field, B. J. Raphael |
| AliGROOVE | Visualisation of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support | Identification of single taxa which show predominately randomized sequence similarity in comparison with other taxa in a multiple sequence alignment and evaluation of the reliability of node support in a given topology | Patrick Kรผck, Sandra A Meid, Christian Groร, Bernhard Misof, Johann Wolfgang Wรคgele. |
| ape | R-Project package for analysis of phylogenetics and evolution | Provides a large variety of phylogenetics functions | Maintainer: Emmanuel Paradis |
| Armadillo Workflow Platform | Workflow platform dedicated to phylogenetic and general bioinformatic analysis | Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows | E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov |
| BAli-Phy | Simultaneous Bayesian inference of alignment and phylogeny | Bayesian inference, alignment as well as tree search | M.A. Suchard, B. D. Redelings |
| BATWING | Bayesian Analysis of Trees With Internal Node Generation | Bayesian inference, demographic history, population splits | I. J. Wilson, Weale, D.Balding |
| BayesPhylogenies | Bayesian inference of trees using Markov chain Monte Carlo methods | Bayesian inference, multiple models, mixture model (auto-partitioning) | M. Pagel, A. Meade |
| BayesTraits | Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available | Trait analysis | M. Pagel, A. Meade |
| BEAST | Bayesian Evolutionary Analysis Sampling Trees | Bayesian inference, relaxed molecular clock, demographic history | A. J. Drummond, M. A. Suchard, D Xie & A. Rambaut |
| BioNumerics | Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data | Neighbor-joining, maximum parsimony, UPGMA, maximum likelihood, distance matrix methods,... Calculation of the reliability of trees/branches using bootstrapping, permutation resampling or error resampling | L. Vauterin & P. Vauterin. |
| Bosque | Integrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignments | Distance and maximum likelihood methods (through PhyML, PHYLIP, Tree-Puzzle) | S. Ramirez, E. Rodriguez. |
| BUCKy | Bayesian concordance of gene trees | Bayesian concordance using modified greedy consensus of unrooted quartets | C. Anรฉ, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey |
| Canopy | Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing | Maximum Likelihood, Markov Chain Monte Carlo (MCMC) methods | Y. Jiang, Y. Qiu, A. J. Minn, and N. R. Zhang |
| CGRphylo | CGR method for accurate classification and tracking of rapidly evolving viruses | Chaos Game Representation (CGR) method, based on concepts of statistical physics | Amarinder Singh Thind, Somdatta Sinha |
| CITUP | Clonality Inference in Tumors Using Phylogeny | Exhaustive search, Quadratic Integer Programming (QIP) | S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp |
| CladoGraph | The main goal of Cladograph is to provide a user-friendly tool for students, teachers, and researchers to explore evolutionary relationships between different species. | Trait analisys | Pedro Andrade Giroldo |
| ClustalW | Progressive multiple sequence alignment | Distance matrix/nearest neighbor | Thompson et al. |
| CoalEvol | Simulation of DNA and protein evolution along phylogenetic trees (that can also be simulated with the coalescent) | Simulation of multiple sequence alignments of DNA or protein sequences | M. Arenas, D. Posada |
| CodABC | Coestimation of substitution, recombination and dN/dS in protein sequences | Approximate Bayesian computation | M. Arenas, J.S. Lopes, M.A. Beaumont, D. Posada |
| Dendroscope | Tool for visualizing rooted trees and calculating rooted networks | Rooted trees, tanglegrams, consensus networks, hybridization networks | Daniel Huson et al. |
| EXACT | EXACT is based on the perfect phylogeny model, and uses a very fast homotopy algorithm to evaluate the fitness of different trees, and then it brute forces the tree search using GPUs, or multiple CPUs, on the same or on different machines | Brute force search and homotopy algorithm | Jia B., Ray S., Safavi S., Bento J. |
| EzEditor | EzEditor is a java-based sequence alignment editor for rRNA and protein coding genes. It allows manipulation of both DNA and protein sequence alignments for phylogenetic analysis | Multiple sequence alignment and editing | Y.-S. Jeon, K. Lee, S.-C. Park, B.-S. Kim, Y.-J. Cho, S.-M. Ha, and J. Chun |
| fastDNAml | Optimized maximum likelihood (nucleotides only) | Maximum likelihood | G.J. Olsen |
| FastTree 2 | Fast phylogenetic inference for alignments with up to hundreds of thousands of sequences | Approximate maximum likelihood | M.N. Price, P.S. Dehal, A.P. Arkin |
| fitmodel | Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selection | Maximum likelihood | S. Guindon |
| Geneious | Geneious provides genome and proteome research tools | Neighbor-joining, UPGMA, MrBayes plugin, PhyML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin | A. J. Drummond, M.Suchard, V.Lefort et al. |
| HyPhy | Hypothesis testing using phylogenies | Maximum likelihood, neighbor-joining, clustering techniques, distance matrices | S.L. Kosakovsky Pond, S.D.W. Frost, S.V. Muse |
| INDELible | Simulation of DNA/protein sequence evolution | Simulation | W. Fletcher, Z. Yang |
| IQPNNI | Iterative ML treesearch with stopping rule (No longer maintained; superseded by IQ-TREE) | Maximum likelihood, neighbor-joining | L.S. Vinh, A. von Haeseler, B.Q. Minh |
| IQ-Tree | An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and Tree-Puzzle | Maximum likelihood, model selection, partitioning scheme finding, AIC, AICc, BIC, ultrafast bootstrapping, branch tests, tree topology tests, likelihood mapping | Lam-Tung Nguyen, O. Chernomor, H.A. Schmidt, A. von Haeseler, B.Q. Minh |
| jModelTest 2 | A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution | Maximum likelihood, AIC, BIC, DT, hLTR, dLTR | D. Darriba, GL. Taboada, R. Doallo, D. Posada |
| JolyTree | An alignment-free bioinformatics procedure to infer distance-based phylogenetic trees from genome assemblies, specifically designed to quickly infer trees from genomes belonging to the same genus | MinHash-based pairwise genome distance, Balanced Minimum Evolution (BME), ratchet-based BME tree search, Rate of Elementary Quartets | A. Criscuolo |
| LisBeth | Three-item analysis for phylogenetics and biogeography | Three-item analysis | J. Ducasse, N. Cao & R. Zaragรผeta-Bagils |
| MEGA | Molecular Evolutionary Genetics Analysis | Distance, Parsimony and Maximum Composite Likelihood Methods | Tamura K, Dudley J, Nei M & Kumar S |
| MegAlign Pro | MegAlign Pro is part of DNASTAR's Lasergene Molecular Biology package. This application performs multiple and pairwise sequence alignments, provides alignment editing, and generates phylogenetic trees. | Maximum Likelihood (RAxML) and Neighbor-Joining | DNASTAR |
| Mesquite | Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern comparative analyses or population genetics, while others do non-phylogenetic multivariate analysis. It can also be used to build timetrees incorporating a geological timescale, with some optional modules. | Maximum parsimony, distance matrix, maximum likelihood | Wayne Maddison and D. R. Maddison |
| MetaPIGA2 | Maximum likelihood phylogeny inference multi-core program for DNA and protein sequences, and morphological data. Analyses can be performed using an extensive and user-friendly graphical interface or by using batch files. It also implements tree visualization tools, ancestral sequences, and automated selection of best substitution model and parameters. | Maximum likelihood, stochastic heuristics (genetic algorithm, metapopulation genetic algorithm, simulated annealing, etc.), discrete Gamma rate heterogeneity, ancestral state reconstruction, model testing | Michel C. Milinkovitch and Raphaรซl Helaers |
| MicrobeTrace | MicrobeTrace is a free, browser-based web application. | 2D and 3D network visualization tool, Neighbor-joining tree visualization, Gantt charts, bubbles charts, networks visualized on maps, flow diagrams, aggregate tables, epi curves, histograms, alignment viewer, and much more. | Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, Roxana Cintron, William M. Switzer |
| MNHN-Tree-Tools | MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. | Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. | Thomas Haschka, Loรฏc Ponger, Christophe Escudรฉ and Julien Mozziconacci |
| Modelgenerator | Model selection (protein or nucleotide) | Maximum likelihood | Thomas Keane |
| MOLPHY | Molecular phylogenetics (protein or nucleotide) | Maximum likelihood | J. Adachi and M. Hasegawa |
| MorphoBank | Web application to organize trait data (morphological characters) for tree building | for use with Maximum Parsimony (via the CIPRES portal), Maximum Likelihood, and Bayesian analysis) | O'Leary, M. A., and S. Kaufman, also K. Alphonse |
| MrBayes | Posterior probability estimation | Bayesian inference | J. Huelsenbeck, et al. |
| Network | Free Phylogenetic Network Software | Median Joining, Reduced Median, Steiner Network | A. Roehl |
| Nona | Phylogenetic inference | Maximum parsimony, implied weighting, ratchet | P. Goloboff |
| OrientAGraph | Admixture graph reconstruction from allele frequencies | f2-statistics or covariance matrix, maximum likelihood network orientation search implemented within TreeMix | Erin Molloy, Arun Durvasula, Sriram Sankararaman |
| PAML | Phylogenetic analysis by maximum likelihood | Maximum likelihood and Bayesian inference | Z. Yang |
| ParaPhylo | Computation of gene and species trees based on event-relations (orthology, paralogy) | Cograph-Editing and Triple-Inference | Hellmuth |
| PartitionFinder | Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments | Maximum likelihood, AIC, AICc, BIC | R. Lanfear, B Calcott, SYW Ho, S Guindon |
| PASTIS | R package for phylogenetic assembly | R, two-stage Bayesian inference using MrBayes 3.2 | Thomas et al. 2013 |
| PAUP* | Phylogenetic analysis using parsimony (*and other methods) | Maximum parsimony, distance matrix, maximum likelihood | D. Swofford |
| phangorn | Phylogenetic analysis in R | ML, MP, distance matrix, bootstrap, phylogentic networks, bootstrap, model selection, SH-test, SOWH-test | Maintainer: K. Schliep |
| Phybase | an R package for species tree analysis | phylogenetics functions, STAR, NJst, STEAC, maxtree, etc | L. Liu & L. Yu |
| phyclust | Phylogenetic Clustering (Phyloclustering) | Maximum likelihood of Finite Mixture Modes | Wei-Chen Chen |
| PHYLIP | PHYLogeny Inference Package | Maximum parsimony, distance matrix, maximum likelihood | J. Felsenstein |
| phyloT | Generates phylogenetic trees in various formats, based on NCBI taxonomy | none | I. Letunic |
| PhyloQuart | Quartet implementation (uses sequences or distances) | Quartet method | V. Berry |
| PhyloWGS | Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors | MCMC | A. G. Deshwar, S. Vembu, C. K. Yung, G. H. Jang, L. Stein, and Q. Morris |
| PhyML | Fast and accurate estimation of phylogenies using maximum likelihood | Maximum likelihood | S. Guindon & O. Gascuel |
| phyx | Unix/Linux command line phylogenetic tools | Explore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs) | J.W. Brown, J.F. Walker, and S.A. Smith |
| POY | A phylogenetic analysis program that supports multiple kinds of data and can perform alignment and phylogeny inference. A variety of heuristic algorithms have been developed for this purpose | Maximum parsimony, Maximum likelihood, Chromosome rearrangement, discreet characters, continuous characters, Alignment | A. Varon, N. Lucaroni, L. Hong, W. Wheeler |
| ProtASR2 | Ancestral reconstruction of protein sequences accounting for folding stability | Maximum likelihood, substitution models | M. Arenas, U. Bastolla |
| ProtEvol | Simulation of protein sequences under structurally constrained substitution models | Simulating sequences, substitution models | M. Arenas, A. Sanchez-Cobos, U. Bastolla U |
| ProteinEvolver | Simulation of protein sequences along phylogenies under empirical and structurally constrained substitution models of protein evolution | Simulating sequences forward in time, substitution models | M. Arenas, H.G. Dos Santos, D. Posada, U. Bastolla |
| ProteinEvolverABC | Coestimation of recombination and substitution rates in protein sequences | Approximate Bayesian computation | M. Arenas |
| ProteinModelerABC | Selection among site-dependent structurally constrained substitution models of protein evolution | Approximate Bayesian computation | D. Ferreiro et al |
| ProtTest3 | A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences | Maximum likelihood, AIC, BIC, DT | D. Darriba, GL. Taboada, R. Doallo, D. Posada |
| PyCogent | Software library for genomic biology | Simulating sequences, alignment, controlling third party applications, workflows, querying databases, generating graphics and phylogenetic trees | Knight et al. |
| QuickTree | Tree construction optimized for efficiency | Neighbor-joining | K. Howe, A. Bateman, R. Durbin |
| RAxML-HPC | Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) | Maximum likelihood, simple Maximum parsimony | A. Stamatakis |
| RAxML-NG | Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next Generation | Maximum likelihood, simple Maximum parsimony | A. Kozlov, D. Darriba, T. Flouri, B. Morel, A. Stamatakis |
| SEMPHY | Tree reconstruction using the combined strengths of maximum-likelihood (accuracy) and neighbor-joining (speed). SEMPHY has become outdated. The authors now refer users to RAxML, which is superior in accuracy and speed. | A hybrid maximum-likelihood โ neighbor-joining method | M. Ninio, E. Privman, T. Pupko, N. Friedman |
| SGWE | Simulation of genome-wide evolution along phylogenetic trees | Simulating genome-wide sequences forward time | Arenas M., Posada D. |
| SimPlot++ | Sequence similarity plots (SimPlots), detection of intragenic and intergenic recombination events, bootscan analysis and sequence similarity networks | SimPlot using different nucleotide/protein distance models; Phi, ฯ2 and NSS recombination tests; Sequence similarity network analysis | S. Samson, E. Lord, V. Makarenkov |
| sowhat | Hypothesis testing | SOWH test | Samuel H Church, Joseph F Ryan, and Casey W Dunn |
| Splatche3 | Simulation of genetic data under diverse spatially explicit evolutionary scenarios | Coalescent, molecular evolution, DNA sequences, SNPs, STRs, RFLPs | M. Currat et al. |
| SplitsTree | Tree and network program | Computation, visualization and exploration of phylogenetic trees and networks | D.H. Huson and D. Bryant |
| TNT | Phylogenetic inference | Parsimony, weighting, ratchet, tree drift, tree fusing, sectorial searches | P. A. Goloboff, J. S. Farris, and K. C. Nixon |
| TOPALi | Phylogenetic inference | Phylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis | Iain Milne, Dominik Lindner et al. |
| TreeGen | Tree construction given precomputed distance data | Distance matrix | ETH Zurich |
| TreeAlign | Efficient hybrid method | Distance matrix and approximate parsimony | J. Hein |
| TreeLine | Tree construction algorithm within the DECIPHER package for R | Maximum likelihood, maximum parsimony, and distance | E. Wright |
| Treefinder | Fast ML tree reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, tree manipulation and visualization, computation of sitewise rates, sequence simulation, many models of evolution (DNA, protein, rRNA, mixed protein, user-definable), GUI and scripting language | Maximum likelihood, distances, and others | Jobb G, von Haeseler A, Strimmer K |
| TreeMix | Admixture graph reconstruction from allele frequencies | f2-statistics or covariance matrix, maximum likelihood, heuristic search (building tree via randomized taxon addition and then adding admixture edges) | Joseph K. Pickrell and Jonathan K. Pritchard |
| Tree-Puzzle | Maximum likelihood and statistical analysis (No longer maintained; superseded by IQ-TREE) | Maximum likelihood | H. A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler |
| TREE-QMC | Summarizes unrooted gene trees into unrooted species tree | Graph-cut-based heuristic for maximum quartet support species tree problem | Yunheng Han, Erin Molloy |
| T-REX (Webserver) | Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignment | Distance (neighbor joining), Parsimony and Maximum likelihood (PhyML, RAxML) tree inference, MUSCLE, MAFFT and ClustalW sequence alignments and related applications | Boc A, Diallo AB, Makarenkov V |
| UShER | Phylogenetic placement using maximum parsimony for viral genomes | Maximum parsimony | Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D and Corbett-Detig R |
| UGENE | Fast and free multiplatform tree editor | GUI with PHYLIP 3.6 and IQTree algorithms | Unipro |
| VeryFastTree | A highly-tuned tool that uses parallelizing and vectorizing strategies to speed inference of phylogenies for huge alignments | Approximate maximum likelihood | Cรฉsar Piรฑeiro. Josรฉ M. Abuรญn and Juan C. Pichel |
| Winclada | GUI and tree editor (requires Nona) | Maximum parsimony, ratchet | K. Nixon |
| Xrate | Phylo-grammar engine | Rate estimation, branch length estimation, alignment annotation | I. Holmes |
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