| Dendroscope |
Free for academic use |
NeXML, Nexus or Newick format |
Assign color individually (Edit>Format) |
N/A |
.eps,. svg,. png,. jpg,. gif,. bmp,. pdf |
Rectangular, slanted, circular and radial views |
1. Supports general functionalities for tree. algorithms, subtree collapse, coloring and re-rooting. 2. Shows tanglegram for two trees or networks. |
Not favorable for users to assign color based on a group of sequences |
| iTOL (interactive tree of life) |
Online version, free |
Newick, Nexus or PhyloXML |
No graphic interface of colorizing function for branches and nodes |
N/A |
.svg,. png,. eps,. pdf |
Rectangularand circular-ring views |
1. Is flexible for users who need to construct a phylogeny based on well-known organisms with NCBI taxonomy IDs. 2. Clade could be collapsed by setting proportion of distance. |
View online only; Not favorable for users to assign the color of subtrees or a group of sequences |
| HyperTree |
Free for academic use |
PHYLIP, phyloXML, Newick |
Assign color individually by graphic inferface (Edit>Color) or color editing file |
N/A |
PHYLIP format |
Linear, radial, unrooted views |
1. Contains simple interface and functionalities for users to draw and colorize a phylogeny 2. Users can re-root the phylogeny by selecting a given node |
Lack of important information in phylogenetics such as branch length, confidence value, node annotation |
| NJPlot |
Free for academic use |
Newick |
N/A |
N/A |
.pdf and. eps |
Rectangular |
Tree operations, including new outgroup assignment, rotation and subtree visualization, are useful for phylogenic display |
Limited functionality and not recommended for large datasets |
| HyperGeny |
Free for academic use, online and downloadable packages are both available |
Newick |
Can only assign one color for all nodes |
N/A |
Newick format |
Unrooted view |
1. Can collapse the subtree and output the Newick file from chosen node. 2. Is available for large tree structures and datasets |
Only for hyperbolic visualization |
| CTree |
Free |
Newick |
Can assign color to selected subtree |
N/A |
.pdf, Newick format |
Rectangular and unrooted views |
1. Has simplistic interface for user to generate a publishable tree along with distance, bootstrapping value, re-rooting and subtree colorization. 2. Comes with statistical analysis, such as calculation of subtype diversity ratio and subtype diversity variance distribution. |
1. Lacks ability to handle large datasets. 2. Supports the input and output format only in Newick format and pdf file, respectively |
| Phylowidget |
Free, online and downloadable packages are both available |
Newick, NHX and Nexus |
Assigns color individually by graphic interface |
N/A |
.jpeg,. pdf,. png |
Rectangular, slanted, circular and unrooted trees |
1. Has comprehensive visualization tool for reconstructing phylogenetic trees. 2. Can handle big datasets |
1. Takes more time and memory to run the program. 2. Lacks intuitive color assignment for sequences |
| BAOBAB |
Free for academic use |
Newick, Nexus or XML format |
Can assign color for subtree based on attributes of sequence name |
N/A |
Newick, XML and Pag |
Rectangular and unrooted trees |
1. Can add, delete or modify the node and/or tree structure. Is useful in generating an artificial tree to illustrate user ideas. 2. Color selection is useful for users who are familiar with color manager function. |
1. Is not very intuitive in assigning the color of nodes and branches. 2. Has simple interface but lacks functionality, such as different tree layouts, topology algorithms |
| TreeIllustrator |
Free for academic use |
Newick, NEXUS |
N/A |
N/A |
.ps and. jpeg |
Phylogram, rectangular, radial and slanted cladograms |
1. Has built-in tree of life browser and search engine. 2. Customizes phylogenetic trees and compares them with the current classification of organisms. |
Lacks annotating functionalities for sequence, such as branch length, nodes and confidence values |
| Archaeopteryx |
Free for academic use |
New Hampshire, Nexus, ToL response XML, or (deprecated) NHX format |
Color assigned in XML format |
N/A |
Newick, PHYLIP,. pdf,. gif,. jpeg,. png,. bmp |
Rectangular, unrooted, and circular trees |
1. Displays features based on taxonomy. 2. Can show node events with size of subtree, number of taxonomies and duplications. |
Lacks graphic interface of color function for branches and nodes |
| MixtureTree Annotator |
Free for academic use |
Newick format |
Can easily assign the color based on the name of sequence in the color function |
Can annotate where and when the nucleotide substitution occurred in given sequence on the tree structure |
NEXUS, Newick format; graphic output including. eps,. pdf,. jpeg,. png,. emf,. gif,. raw,. bmp,. ps |
Rectangular, polar, radial trees |
1. Easily incorporates colorization and mutation annotating function into FigTree phylogeny viewer. 2. Has intuitive interface for users to assign color to nodes and branches; automatically groups the sequences based on the names of sequences. 3. Has accessible view of every mutation event on tree layouts |
1. Cannot collapse clade 2. Cannot integrate the taxonomy of organisms based on known classifications |
