Phylogenetic Tree
- CompareTrees 4 – Compare Phylogenetic Trees
- Ktreedist 1.0 – Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees
- iTOL 2.2.1 / iTOL Toolbar for Mozilla Firefox 1.0.5 – Display & Manipulation of Phylogenetic Trees
- RAxML 7.4.2 / RAxML Workbench 1.0 – Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees
- AST 0.4 – Automated sequences Sampling method over Taxa for Generating more Informative Phylogenetic Trees
- Archaeopteryx 0.9809 – Visualization, Analysis & Editing of Phylogenetic Trees
- Dendroscope 3.2.4 – Visualize Phylogenetic Trees & Rooted Networks
- IQ-TREE 0.9.4 – Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation
- RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program
- Treevolution 1.2 – Visual Analysis of Phylogenetic Trees
- SeaView 4.4.1 – Sequence Alignment and Phylogenetic Tree Building
- TreeSnatcher Plus 201206 – Phylogenetic Tree Capturing Tool
- TIQ 1.0 – Browse Phylogenetic Trees of Toxins
- 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
- TreeTest – Testing Phylogenetic Tree Topologies in a Frequentist Framework
- Phyrex 1.1 – Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees
- NJplot 2.4 – Phylogenetic Tree Drawing Program
- jsPhyloSVG 1.55 – Javascript Library for Visualizing Interactive & Vector-based Phylogenetic Trees
- Mowgli – Phylogenetic Tree Reconciliation Program
- Phylo3D 1.2 – Convert Phylogenetic Trees File into LibSea format
- CTree 1.03 – Analysis of Clusters on Phylogenetic Trees
- 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
- HyperTree 1.2.2 – Java Phylogenetic Tree Viewer
- PhyloWidget – View, Edit, and Publish Phylogenetic Trees
- RandomTaxa 1.0 – Select at Random Taxa from a Phylogenetic Tree and Output the reduced tree
- MLtree 1.0 – Maximum Likelihood Model Estimation for Phylogenetic Trees
- Consel 0.20 – Assess Confidence of Phylogenetic Tree Selection
- IQPNNI 3.3.2 – Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data
- phylo 0.3 – Phylogenetic Tree Viewer
- NewickReader 1.0 – Produce Distance Matrix from Branch Lengths in Phylogenetic Tree
- DistanceCorrelations 1.0 – Correlate Data Matrix with Branch Lengths of Phylogenetic Tree
- Treecon-Tools 0.1 – Convert Phylogenetic Trees File Formate
- UpdownDistance – Tool for comparing phylogenetic trees
- Fdur – Compute Sufficient Statistics of Phylogenetic Tree Models
- JTreeView 0.8 – Java based Phylogenetic Tree Viewer
- FamFetch 2.0 – Search for Tree Patterns in Databases of Phylogenetic Trees
- newicktree 1.1 – LaTeX package for Drawing of Phylogenetic Trees
- mswordtree 1.0 – MS Word Macro for Drawing of Phylogenetic Trees
- Leaphy 1.0 beta – Phylogenetic Tree Estimation Software
- PoInTree 1.0.1.2 – Polar and Interactive Phylogenetic Tree
- Baobab 3.31 – Editor for Large Phylogenetic Trees
- TreeEdit 1.0a10 – Organize, View & Manipulate sets of Phylogenetic Trees
- FigTree 1.3.1 – Produce Figures of Phylogenetic Trees
- NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data
- ProfDistS 0.9.9 beta – Construction of Large Phylogenetic Trees
- T-REX 4.01 – Reconstruct Phylogenetic Trees and Reticulation Networks
- TreeViewJ 1.1.2 – View & Analyze Phylogenetic Trees
- TreeViewX 0.5.1 – Program to Display Phylogenetic Trees
- TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model
- ArboDraw 2006 – Phylogenetic Tree Builder & Viewer
- Phylodendron 0.8d – Phylogenetic Tree Drawing
- TreeGraph 2.0.47 – Graphical Editor for Phylogenetic Trees
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