List of phylogenetics software

! Name

! Description

| R software package that contains the qpGraph, qpAdm, qpWave, and qpDstat programs

|

| Nick Patterson, David Reich

|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

| Workflow platform dedicated to phylogenetic and general bioinformatic analysis

| Simultaneous Bayesian inference of alignment and phylogeny

| Bayesian Analysis of Trees With Internal Node Generation

| Bayesian inference of trees using Markov chain Monte Carlo methods

| Analyses trait evolution among groups of species for which a phylogeny or sample of phylogenies is available

| Bayesian Evolutionary Analysis Sampling Trees

| Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data

| Integrated graphical software to perform phylogenetic analyses, from the importing of sequences to the plotting and graphical edition of trees and alignments

| Bayesian concordance of gene trees

|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

|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

|Clonality Inference in Tumors Using Phylogeny

|Exhaustive search, Quadratic Integer Programming (QIP)

|S. Malikic, A.W. McPherson, N. Donmez, C.S. Sahinalp

| Progressive multiple sequence alignment

|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

|Coestimation of substitution, recombination and dN/dS in protein sequences

|Approximate Bayesian computation

|M. Arenas, J.S. Lopes, M.A. Beaumont, D. Posada

| Tool for visualizing rooted trees and calculating rooted networks

| 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

| 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

| Optimized maximum likelihood (nucleotides only)

| Fast phylogenetic inference for alignments with up to hundreds of thousands of sequences

| Fits branch-site codon models without the need of prior knowledge of clades undergoing positive selection

| Geneious provides genome and proteome research tools

| Hypothesis testing using phylogenies

|Simulation of DNA/protein sequence evolution

|Simulation

|W. Fletcher, Z. Yang

| Iterative ML treesearch with stopping rule

| An efficient phylogenomic software by maximum likelihood, as successor of IQPNNI and Tree-Puzzle

| A high-performance computing program to carry out statistical selection of best-fit models of nucleotide substitution

| 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

| Three-item analysis for phylogenetics and biogeography

| Molecular Evolutionary Genetics Analysis

|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 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 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.

|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{{Cite journal|last1=Campbell|first1=Ellsworth M.|last2=Boyles|first2=Anthony|last3=Shankar|first3=Anupama|last4=Kim|first4=Jay|last5=Knyazev|first5=Sergey|last6=Cintron|first6=Roxana|last7=Switzer|first7=William M.|date=2021-09-07|title=MicrobeTrace: Retooling molecular epidemiology for rapid public health response|journal=PLOS Computational Biology|language=en|volume=17|issue=9|pages=e1009300|doi=10.1371/journal.pcbi.1009300|issn=1553-7358|pmc=8491948|pmid=34492010|bibcode=2021PLSCB..17E9300C |doi-access=free}}

|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, Loïc Ponger, Christophe Escudé and Julien Mozziconacci{{Cite journal |last1=Haschka |first1=Thomas |last2=Ponger |first2=Loic |last3=Escudé |first3=Christophe |last4=Mozziconacci |first4=Julien |date=2021-06-08 |title=MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences |url=https://doi.org/10.1093/bioinformatics/btab430 |journal=Bioinformatics |volume=37 |issue=21 |pages=3947–3949 |doi=10.1093/bioinformatics/btab430 |pmid=34100911 |issn=1367-4803}}

| Model selection (protein or nucleotide)

| Molecular phylogenetics (protein or nucleotide)

|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,{{Cite journal|last1=O'Leary|first1=Maureen A.|last2=Kaufman|first2=Seth|date=October 2011|title=MorphoBank: phylophenomics in the "cloud"|journal=Cladistics|language=en|volume=27|issue=5|pages=529–537|doi=10.1111/j.1096-0031.2011.00355.x|pmid=34875801 |s2cid=76652345|doi-access=free}} also K. Alphonse

| Posterior probability estimation

| Free Phylogenetic Network Software

| Phylogenetic inference

| Admixture graph reconstruction from allele frequencies

| f2-statistics or covariance matrix, maximum likelihood network orientation search implemented within TreeMix {{cite journal |last1=Pickrell |first1=Joseph K. |last2=Pritchard |first2=Jonathan K. |title=Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data |journal=PLOS Genetics |date=15 November 2012 |volume=8 |issue=11 |pages=e1002967 |doi=10.1371/journal.pgen.1002967 |doi-access=free |pmid=23166502 |pmc=3499260 }}

| Erin Molloy, Arun Durvasula, Sriram Sankararaman {{cite journal |last1=Molloy |first1=Erin K |last2=Durvasula |first2=Arun |last3=Sankararaman |first3=Sriram |title=Advancing admixture graph estimation via maximum likelihood network orientation |journal=Bioinformatics |date=12 July 2021 |volume=37 |issue=Supplement_1 |pages=i142–i150 |doi=10.1093/bioinformatics/btab267 |pmc=8336447 }}

| Phylogenetic analysis by maximum likelihood

| Computation of gene and species trees based on event-relations (orthology, paralogy)

| Combined selection of models of molecular evolution and partitioning schemes for DNA and protein alignments

|R package for phylogenetic assembly

|R, two‐stage Bayesian inference using MrBayes 3.2

|Thomas et al. 2013{{Cite journal|last1=Thomas|first1=Gavin H.|last2=Hartmann|first2=Klaas|last3=Jetz|first3=Walter|last4=Joy|first4=Jeffrey B.|last5=Mimoto|first5=Aki|last6=Mooers|first6=Arne O.|date=2013|title=PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences|journal=Methods in Ecology and Evolution|language=en|volume=4|issue=11|pages=1011–1017|doi=10.1111/2041-210X.12117|bibcode=2013MEcEv...4.1011T |s2cid=86694418 |issn=2041-210X}}

| Phylogenetic analysis using parsimony (*and other methods)

| Phylogenetic analysis in R

| Phylogenetic Clustering (Phyloclustering)

| PHYLogeny Inference Package

| Generates phylogenetic trees in various formats, based on NCBI taxonomy

| Quartet implementation (uses sequences or distances)

|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

| Fast and accurate estimation of phylogenies using maximum likelihood

| Unix/Linux command line phylogenetic tools

| 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

|Ancestral reconstruction of protein sequences accounting for folding stability

|Maximum likelihood, substitution models

|M. Arenas, U. Bastolla

|Simulation of protein sequences under structurally constrained substitution models

|Simulating sequences, substitution models

|M. Arenas, A. Sanchez-Cobos, U. Bastolla U

|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

|Coestimation of recombination and substitution rates in protein sequences

|Approximate Bayesian computation

|M. Arenas

|Selection among site-dependent structurally constrained substitution models of protein evolution

|Approximate Bayesian computation

|D. Ferreiro et al

| A high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences

| Software library for genomic biology

| Tree construction optimized for efficiency

| Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids)

| Randomized Axelerated Maximum Likelihood for High Performance Computing (nucleotides and aminoacids) Next Generation

| 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.

|Simulation of genome-wide evolution along phylogenetic trees

|Simulating genome-wide sequences forward time

|Arenas M., Posada D.

| Sequence similarity plots (SimPlots{{cite journal |last1=Lole |first1=Kavita S. |last2=Bollinger |first2=Robert C. |last3=Paranjape |first3=Ramesh S. |last4=Gadkari |first4=Deepak |last5=Kulkarni |first5=Smita S. |last6=Novak |first6=Nicole G. |last7=Ingersoll |first7=Roxann |last8=Sheppard |first8=Haynes W. |last9=Ray |first9=Stuart C. |title=Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination |journal=Journal of Virology |date=January 1999 |volume=73 |issue=1 |pages=152–160 |doi=10.1128/JVI.73.1.152-160.1999|pmid=9847317 |pmc=103818}}), detection of intragenic and intergenic recombination events, bootscan analysis{{cite journal |last1=Salminen |first1=Mika O. |last2=Carr |first2=Jean K. |last3=Burke |first3=Donald S. |last4=McCutchan |first4=Francine E. |title=Identification of Breakpoints in Intergenotypic Recombinants of HIV Type 1 by Bootscanning |journal=AIDS Research and Human Retroviruses |date=November 1995 |volume=11 |issue=11 |pages=1423–1425 |doi=10.1089/aid.1995.11.1423 |pmid=8573403}} and sequence similarity networks

|Simulation of genetic data under diverse spatially explicit evolutionary scenarios

|Coalescent, molecular evolution, DNA sequences, SNPs, STRs, RFLPs

|M. Currat et al.

| Tree and network program

| Phylogenetic inference

| Phylogenetic inference

| Tree construction given precomputed distance data

| Efficient hybrid method

| Tree construction algorithm within the DECIPHER package for R

| 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

| 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 {{cite journal |last1=Pickrell |first1=Joseph K. |last2=Pritchard |first2=Jonathan K. |title=Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data |journal=PLOS Genetics |date=15 November 2012 |volume=8 |issue=11 |pages=e1002967 |doi=10.1371/journal.pgen.1002967 |doi-access=free |pmid=23166502 |pmc=3499260 }}

| Maximum likelihood and statistical analysis

| Summarizes unrooted gene trees into unrooted species tree

| Graph-cut-based heuristic for maximum quartet support species tree problem {{cite journal |last1=Snir |first1=Sagi |last2=Rao |first2=Satish |title=Quartet MaxCut: A fast algorithm for amalgamating quartet trees |journal=Molecular Phylogenetics and Evolution |date=1 January 2012 |volume=62 |issue=1 |pages=1–8 |doi=10.1016/j.ympev.2011.06.021 |pmid=21762785 |bibcode=2012MolPE..62....1S }}{{cite journal |last1=Avni |first1=Eliran |last2=Cohen |first2=Reuven |last3=Snir |first3=Sagi |title=Weighted Quartets Phylogenetics |journal=Systematic Biology |date=1 March 2015 |volume=64 |issue=2 |pages=233–242 |doi=10.1093/sysbio/syu087 |pmid=25414175 }}

| Yunheng Han, Erin Molloy {{cite journal |last1=Han |first1=Yunheng |last2=Molloy |first2=Erin K |title=Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC |journal=Systematic Biology |date=25 February 2025 |pages=syaf009 |doi=10.1093/sysbio/syaf009 |pmid=40000439 }}{{cite journal |last1=Han |first1=Yunheng |last2=Molloy |first2=Erin K. |title=Improving quartet graph construction for scalable and accurate species tree estimation from gene trees |journal=Genome Research |date=1 July 2023 |volume=33 |issue=7 |pages=1042–1052 |doi=10.1101/gr.277629.122 |pmid=37197990 |pmc=10538498 }}

| Tree inference and visualization, Horizontal gene transfer detection, multiple sequence alignment

| Phylogenetic placement using maximum parsimony for viral genomes

| Fast and free multiplatform tree editor

|A highly-tuned tool that uses parallelizing and vectorizing strategies to speed inference of phylogenies for huge alignments

|Approximate maximum likelihood

|César Piñeiro. José M. Abuín and Juan C. Pichel

| GUI and tree editor (requires Nona)

| Phylo-grammar engine