Phylogenetic Analysis
- CompareTrees 4 – Compare Phylogenetic Trees
- phyloBreak – Gene Genealogy Simulator for Phylogeographic Study
- SPIDIR 0.9 – Species Informed Distance-based Reconstruction
- SPIMAP 1.1 – Species Informed Maximum A Posteriori Gene Tree Reconstruction
- DLCoal 1.0 – Modeling Gene Duplications, Losses, and Coalescence
- STAR-MP 1.0 – Species Tree informed Architecture Reconstruction – Maximum Parsimon
- TreeFix 1.1.7 / TreeFix-DTL 1.0.0 – Statistically Informed Gene Tree Error Correction using Species Trees
- RANGER-DTL 1.0 – Rapid ANalysis of Gene family Evolution using Reconciliation-DTL
- Notung 2.6 – Date Gene Duplications and Optimizing Gene Family Trees
- Taxy / Taxy-Pro – Fast Estimation of Metagenomic Taxon Abundances
- MEGA 5.2 – Molecular Evolutionary Genetics Analysis
- Ktreedist 1.0 – Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees
- Gblocks 0.91b – Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis
- PhyloMatch 1.0 – Discover highly Phylogenetically informative Genes in Sequenced Genomes
- iTOL 2.2.1 / iTOL Toolbar for Mozilla Firefox 1.0.5 – Display & Manipulation of Phylogenetic Trees
- phytools 0.2-40 – Phylogenetic Tools in R
- RAxML 7.4.2 / RAxML Workbench 1.0 – Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees
- PAINT 1.0_beta60 – Phylogenetic Annotation and INference Tool
- SATé 2.2.7 – Simultaneous Alignment and Tree Estimation
- SPRSupertrees 1.1.1 – Calculate Rooted Supertrees that Minimize the SPR Distance.
- rSPR 1.1.1 – Calculate Rooted Subtree-prune-and-regraft Distances and rooted agreement forest
- EBD 1.0.3 – Taxon- and Phylogenetic-based Beta Diversity Measures
- phyclust 0.1-14 – Phylogenetic Clustering
- PhyloSim 2.0.1 – Monte Carlo Simulation of Sequence Evolution
- AST 0.4 – Automated sequences Sampling method over Taxa for Generating more Informative Phylogenetic Trees
- FastTree 2.1.7 – Cmpute Large Minimum Evolution Trees with Profiles
- Archaeopteryx 0.9809 – Visualization, Analysis & Editing of Phylogenetic Trees
- forester 1.027 – Software Libraries for Phylogenomics and Evolutionary Biology Research
- phyutility 2.6 – Phyloinformatic Utility for Trees, Alignments, and Molecular data
- ADAPTSITE 1.6 – Detect Natural Selection at Single Amino Acid Sites
- PhyloBayes 3.3f – Bayesian Phylogenetic software based on Mixture Models
- Dendroscope 3.2.4 – Visualize Phylogenetic Trees & Rooted Networks
- ANCML 1.0 – Ancestor States using Maximum Likelihood
- DensiTree 2.1.7 – Qualitative Analysis of Sets of Trees
- Phylomarker 3.0 – Mining Phylogenetic Markers for Assembling the Tree of Life
- TESS 1.2.0 – Simulation of Reconstructed Phylogenetic Trees under Time-dependent Birth-death Processes
- RevBayes 1.0.0 beta2 – Bayesian Inference of Phylogeny
- PATHd8 – Phylogenetic Dating of Large Trees without Molecular Clock
- MrModelfit 1.2/ Modelfit 1.2 – Perl script for running MrModeltest2/Modeltest
- Mailfit 0.2 – Perl script that runs PAUP and MrModeltest2
- Burntrees 0.2.1 – Perl script for manipulating MrBayes tree and Parameter files
- MrModeltest 2.3 – C program for selecting DNA substitution models using PAUP*
- MrAIC 1.4.5 / pMrAIC 1.1 – Perl script for selecting DNA substitution models using PHYML
- PluMiST 1.1 – Plus and Minus SuperTrees
- IQ-TREE 0.9.4 – Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation
- PhyRe – Evaluate Taxon Sampling in Evolutionary Studies
- RFsupertrees 2.0 – Program for Constructing Accurate Supertrees
- Network 4.611 – Phylogenetic Network Software
- ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection
- Clann 3.2.2 – Construct Phylogenetic Supertrees
- RapidNJ 2.2.1 – Fast Canonical Neighbor-joining Tree Construction
- Fitmodel 20130115- Deciphering the Patterns of Darwinian Selection
- RDP 4.19 Beta – Recombination Detection Program
- ProtTest 3.2.2 – Selection of Best-fit Models of Protein Evolution
- Jevtrace 3.16b – Implementation of Evolutionary Trace
- jMODELTEST 2.1.3 – Phylogenetic Model Averaging
- APE 3.0-8 – Analysis of Phylogenetics and Evolution
- Vanilla 1.2 – Programs to Access Features in PAL
- SplitsTree 4.12.8 – Compute Phylogenetic Networks
- PhyML 20130219 – Phylogeny software based on the Maximum Likelihood
- BEAST 1.7.5 – Bayesian Evolutionary Analysis of Molecular Sequences
- RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program
- Treevolution 1.2 – Visual Analysis of Phylogenetic Trees
- PhylTools 1.32 – Calculate Genetic Distances
- SeaView 4.4.1 – Sequence Alignment and Phylogenetic Tree Building
- PhyloPro – Generation and Visualization of Phylogenetic Profiles across Eukarya
- DrML 1.0 – Maximum Likelihood Estimation in the Duplication Loss Model
- urRF – unrooted Gene Trees vs rooted Species Trees
- Fasturec 20120209 – Local Search algorithms for Gene Tree Parsimony problems
- UREC 1.02 – Unrooted REConciliation
- PICS-Ord 20110823 – Extract Phylogeny Information from hard-to-align Regions of Multiple Sequence Alignments
- SPACoDi 0.1 / spacodiR 0.13.0115 – Structuring of Phylogenetic Diversity
- EPoS 0.91 – Estimating Phylogenies of Species
- phangorn 1.7-1 – Phylogenetic Analysis in R
- PTree 1.1 – Pattern-based, Stochastic Search method for Maximum Parsimony Phylogenies
- GenomeSignatureTree 1.0 – Alignment-free Inference of Genome Trees
- AntigenicTreeTools 1.0 – Infer Antigenic Trees to resolve the Antigenic Impact of Amino Acid Changes
- PhyloPythiaS 1.3 – Web Server for Taxonomic Assignment of Metagenome Sequences
- TreeSnatcher Plus 201206 – Phylogenetic Tree Capturing Tool
- How old is your fold? – The relative age of Superfamilies and Folds
- Patristic – Input different Tree files and computes their Patristic Distances
- TULIP 1.5 – Estimate Molecular Phylogenies according to the TULIP theorem
- CombineTrees – Unite MP Trees into Single Graph
- TIQ 1.0 – Browse Phylogenetic Trees of Toxins
- MANTiS 1.1 – Phylogenetic Framework for Multi-species Genome Comparisons
- MetaPIGA 2.1.3 – Large Phylogeny Estimation
- MirroT 0.1 – Mirroring co-evolving Trees in the light of their Topologies
- chromEvol 1.3 – Analyze Changes in Chromosome-number along a Phylogeny
- nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution
- Unrooted – Draw Binary Tree Expressed in the standard Phylogenetic Tree Format
- RAP – Phylogenetic Tree Reconciler
- PATHGROUPS – Rapid Small Phylogeny
- TreeTest – Testing Phylogenetic Tree Topologies in a Frequentist Framework
- PhyBayes 200208 – Bayesian Inference in Phylogenetics
- AHLC – Adhockeries for Estimating Divergence Times between Species
- CodonPhyML 1.00 – Phylogeny Inference under Codon Models using Maximum Likelihood
- PLEX 0.95 – Phylogenetics, Likelihood, Evolution, and CompleXity
- TARGeT – Tree Analysis of Related Genes and Transposons
- scaleboot 0.3-3 – Approximately Unbiased P-values via Multiscale Bootstrap
- Mirrortree – Interactive study of the Co-evolution of Protein Families
- Phyrex 1.1 – Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees
- PAML 4.6 – Phylogenetic Analysis by Maximum Likelihood
- SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool
- PhyDesign – Phylogenetic Informativeness Analysis
- GPX – Gene Phylogeny eXplorer
- BranchClust 1.01 – A Phylogenetic Algorithm for Selecting Gene Families
- ProPhylo 1.02 – Phylogenetic Profile comparison program using Partial Phylogenetic Profile algorithm
- Phylemon 2.0 – Web-tools for Molecular Evolution, Phylogenetics, Phylogenomics and Hypothesis testing
- FTreeView 1.1.0 – Functional Treeview
- RAxML-Light 1.09 – Strapped down Checkpointable RAxML version for Computing Huge trees
- GSI 0.92 – Genealogical Sorting Index
- DendroPy 3.12.0 – Phylogenetic Computing Library
- GenGIS 2.0.2 – Combine Digital Map data with Genomic Data
- Lagrange 20120508 – Likelihood Analysis of Geographic Range Evolution
- BAli-Phy 2.1.1 – Bayesian Alignment and Phylogeny estimation
- seq-gen-cov – Modification of Seq-gen
- MDL 1.0 – Minimum Description Length for the detection of Phylogenetics Breakpoints
- phylolm 1.0 – R package for Fitting Phylogenetic Linear Regression models
- GZ-gamma – Estimate Parameter of Substitution Rate Variation among Sites
- CAPE – Test Convergent and Parallel Evolution at the Amino Acid sequence level
- ALTREE 1.2.1 – Phylogeny-based Analysis
- PHYMMBL 4.0 – Taxonomically Classifying Metagenomic Short Reads
- Quicktree-SD 1.2 – Implemented Scroredist Distances in Quicktree
- Prunier 2.1 – Detecting Lateral Gene Transfers by Statistical Reconciliation of Phylogenetic Forests
- MirrorT 0.1 – Mirroring Co-evolving Trees in Light of their Topologies
- CoMap 1.4.1 – Map Substitutions on a Phylogeny and Detect Coevolution
- LAMARC 2.1.8 – Maximum Likelihood & Bayesian Estimation of Population Parameters
- Seq-Gen 1.3.3 – Simulate the Evolution of Sequences along a Phylogeny
- BUCKy 1.4.2 – Gene Tree Reconciliation with Bayesian Concordance Analysis
- NJplot 2.4 – Phylogenetic Tree Drawing Program
- jsPhyloSVG 1.55 – Javascript Library for Visualizing Interactive & Vector-based Phylogenetic Trees
- PhyloGena 1.04 – Automated Interactive Phylogenetic Annotation Tool
- LcaMap – Simultaneous Identification of Duplications, Losses and Lateral Gene Transfers
- fastHN – Fast Tool for Minimum Hybridization Networks
- HybridNet – Compute rSPR Distances, Hybridization Numbers, and Hybridization Networks
- ImOSM 20110902 – Imbed model Violation as One Step Mutations into Sequence Alignment
- PhyloDet 1.0 – PhyloDetective tree visualizer
- IDC – Calculation of Independent Contrasts
- pcca – Phylogenetic Canonical Correlation Analysis
- MAPPS 1.1.6 – Determine Nucleotide Model Adequacy
- SIMMAP 1.5.2 – StochastIc Mutational MApping on Phylogenies
- DISPAN – Genetic Distance and Phylogenetic Analysis
- METREE 1.2 – Infer and Test Minimum Evolution Trees
- PHYLTEST 2.0 – Test Phylogenetic Hypothesis
- Statio – Test Stationarity of Base Composition and Models
- TIMER 0.1 – Estimate Divergence Times
- Ancestor – Inference of Ancestral Amino Acid Sequences by the Distance-Based Bayesian Method
- Anc-gene – Inference of Ancestral Gene Sequences by the Distance-Based Bayesian Method
- BN-BS – Estimation of Synonymous and Nonsynonymous Branch Lengths from Pairwise Distances
- FISHER – Fisher’s Exact Test for 2×2 Tables
- NG-new – Modified Nei-Gojobori Method for Computing Synonymous and Nonsynonymous Distances
- RESTDATA – Restriction Data and Phylogenetic Analysis
- GIGA 1.1.1 – Gene Tree Inference in the Genomic Age
- SCIPHY 3.01 – Subfamily Classification In PHYlogenomics
- ANCESCON – ANCEStral sequence reCONstruction
- POPE – Phylogeny, Ortholog and Paralog Extractor
- EMRAE – Efficient Method to Recover Ancestral Events
- Bosque 1.8 – Phylogenetic Analysis Software
- PhyloQuart 1.4 – Reconstruct Phylogenies from Quartets
- ScripTree 17 – Scripting Phylogenetic Graphics
- SSIMUL 1.2 – Speciation SIgnal extraction from MULtigene families
- Gk-arrays 1.0.0 – Data Structure to Index the K-mers in a Collection of Reads
- Mowgli – Phylogenetic Tree Reconciliation Program
- CopyCat 2.02 – Co-phylogenetic Analysis Tool
- HyPhy 2.1.2 – Hypothesis testing using Phylogenies
- TreeThrasher 0.41.1 – Visualize all Trees within TAED
- GRUNT – Grouping Ungrouping Naming Tool
- ModelPie 1.01 – GUI for ModelTest and MrModelTest
- TVi 1.01 – Tree Viewer with Interactions
- CTree 1.03 – Analysis of Clusters on Phylogenetic Trees
- phylotools 0.1.2 – Phylogenetic Tools for Ecologists
- Mavric 0.8.3 – Python toolkit for Phylogenetics
- PornStar 2.0 – Hierarchical Likelihood Ratio Calculator
- Phylocom 4.2 – Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic
- Parsimonator 1.02 – Fast open-source Parsimony program
- PaPaRa 2.0 – PArsimony-based Phylogeny-Aware Read alignment program
- TreeCounter – Compute the Number of possible Rooted and Unrooted Binary Trees
- TCS 1.21 – Phylogenetic Network Estimation using Statistical Parsimony
- Barphlye – Bayesian Analysis of Rearrangement Phylogeny in Yersinia
- Vim Nexus syntax highlighting – Nexus syntax highlighting files for the Vim editor
- codonbias 20060818 – Estimate Selection Coefficients relating to optimal Codon usage
- Ginkgo 3.9.0 – Phylogeographical Evolution Simulator
- NCL 2.1.18 – NEXUS C++ Class Library
- Phycas 1.2.0 – Phylogenetic Analyses
- PhyloGeoRef – Java Library for Mapping Phylogenetic Trees and Geographical Information in KML
- ETE 2.1 – Python Environment for Phylogenetic Tree Exploration
- Radié 1.01 – Character Visualization and Computation Using Radial Phylogenetic Trees
- NetworkDiversity 1.0.0 – Calculation of beta diversity over Phylogenetic Networks
- EEEP 1.01 – Efficient Evaluation of Edit Paths
- GeoPhyloBuilder 1.2.1 – ArcGIS Extension that Creates Geophylogenies
- HyperTree 1.2.2 – Java Phylogenetic Tree Viewer
- PhyloWidget – View, Edit, and Publish Phylogenetic Trees
- GARLI 2.0 – Phylogenetic Analysis of Molecular Sequence data using the Maximum-likelihood Criterion
- SDM – Fast Distance-based Approach for (Super)Tree Building in Phylogenomics
- PhySIC_IST – Cleaning Source Trees to infer more Informative Supertrees
- PhyD* – Fast NJ-like algorithms to deal with incomplete Distance Matrices
- DTdraw – Tandem Duplication History Drawing Program
- DTscore – Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees
- BIONJ – Distance based Phylogeny Reconstruction Algorithm
- DupTree – Large Scale Gene Tree Parsimony Analysis
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