This page provides access to my applet for comparing pairs of alternative phylogenies. The original paper about the algorithm and software was published in Bioinformatics.
A new version of the software has been developed (September 2011). This is much faster than the original and corrects a couple of problems. In addition, the standalone version of the program now provides a command-line interface for batch processing of many trees. The standalone version can be downloaded using the link below. The original version of the software is still available.
The two phylogenies should be specified using Newick strings. Make sure your strings (i) contain branch lengths, (ii) are terminated with a semi-colon, (iii) do not contain bootstrap values or interior labels, and (iv) contain exactly the same set of taxa.
Here are two example trees to try out (paste the data into the boxes above):
| Phylogeny A: | ((((((N_YBF106:0.6875,N_YBF30:0.6875):2.3750,SIVcpzUS:1.9375):0.5, (SIVcpzCAM5:1.3750,SIVcpzCAM3:1.2500):1.1250):1.1250,SIVcpzGAB1:3.1250):0.6250, ((((M_U.83CD003:1.5,M_F.MP411:1.6250):0.1250,M_C.ETH2220:1.5):0.1875,M_A.92UG037:1.3750):0.25, M_D.NDK:1.250):1.6875):1.8750,((O_SEMP1299:1.1250,O_ANT70:1.0):0.4375,O_MVP5180:1.6250):5.0); |
| Phylogeny B: | ((((((SIVcpzCAM5:0.8333,SIVcpzUS:1.8889):0.3333,SIVcpzCAM3:1.3333):1.1111, SIVcpzGAB1:1.3333):0.6666,(N_YBF106:0.5556,N_YBF30:0.8889):1.3333):0.3889, ((((M_F.MP411:1.5556,M_C.ETH2220:1.2222):0.3333,M_D.NDK:1.6667):0.2778, M_U.83CD003:1.0):0.6666,M_A.92UG037:1.0):0.4444):1.5556, ((O_SEMP1299:0.7778,O_ANT70:0.8889):1.0,O_MVP5180:1.0):4.1111); |
Left click on a branch with the mouse to highlight the corresponding branch in the other tree under the 1-to-1 map.
Right click on the background to bring up the configuration menu. This allows you to adjust the size of the tree and change the display options.
Left shift-click on a branch highlights the branch on the other tree that has the overall best score, independent of the 1-to-1 constraint.
Information is displayed at the bottom of the panel. Initially this contains the mean topological score between internal branches under the 1-to-1 map between the trees. Following mouse clicks, scores for the corresponding match are displayed.
If you would like a copy of the Compare2Trees software, type your email address and follow the link below.