RAP is an algorithm and a software have been developed, which permit to find gene duplications in phylogenetic trees, in order to improve gene function inferences. The algorithm is applicable to realistic data, especially n-ary species tree and unrooted phylogenetic tree
RAP-Green is a new implementation and an improvment of the RAP software which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.
PhyloSketch is an interactive program for sketching rooted phylogenetic trees and networks. The program reports on some of mathematical properties of the network. The program can import and export rooted phylogenetic trees or networks in (extended) Newick format.
Dendroscope is a software for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool.
ArboDraw is a program for building and displaying phylogenetic trees of protein and nucleic acid sequences. It can import and display dendrogram files in Newick format (generated by MUSCLE, Phylip, clustalw, etc.). Among the key features are the ability to annotate sequences, and to select and color independently various parts of the tree. A very convenient annotation functionality allows the user to view annotations by placing the mouse above the sequence of interest. Edited and annotated files can be saved and restored at a later time.
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.
Baobab is an editor for large phylogenetic trees written in Java. It allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier.
NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.