The Visual TreeCmp application was designed to compute distances between arbitrary phylogenetic trees. Visual TreeCmp is the first implementation of Matching Split/Cluster/Pair metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. Offers an implementation of metrics with better computational efficiency than available tools, allowing to compare trees with a large number of leaves.

---

rich collection of available phylogenetic metrics

---

The Visual TreeCmp implements eighteen metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees.

Eleven metrics for rooted trees

• Triples metric
• Robinson-Foulds metric based on clusters
• Matching Pair metric
• Nodal Splitted metric with L2 norm
• Matching Cluster metric
• Rooted maximum agreement subtree distance
• Cophenetic metric with L2 norm
• Robinson-Foulds weighted metric based on clusters
• Nodal Splitted weighted metric with L2 norm
• Geodesic rooted distance
• Cophenetic weighted metric with L2 norm

Seven metrics for unrooted trees:

• Quartet distance
• Path difference distance
• Robinson-Foulds distance
• Matching Split distance
• Unrooted maximum agreement subtree distance
• Robinson-Foulds weighted distance
• Geodesic unrooted distance

---

four comparison modes

---

There are four modes of comparing trees available:

• overlapping pair comparison mode - every two neighboring trees in the input file are compared,
• window comparison mode - every two trees within a window with a specified size are compared,
• matrix comparison mode - every two trees in the input file are compared,
• referential trees to all input trees mode - each tree in the input file is compared to all referenced trees.

---

practical additional options

---

We also propose a way to obtain normalized distances between trees, which indicate whether two trees are more dissimilar than two random trees with the same number of leaves according to a given metric. Application allow summarizing for each metric such parameters as: number of compared trees, average value, standard deviation, minimum and the maximum value.

---

multiple forms and additional tool

---

Visual TreeCmp is available in three forms, as:

• command line tool/library (.jar),
• Spring framework Web application (.war),
• standalone application with WEB GUI based on Spring framework (.jar).

Additionally, in Visual TreeCmp package we have included a cross-platform phylogenetic random trees generator (PRTGen) implemented in C++.