Pairwise comparison of phylogenies Newcastle University :: School of Maths and Stats :: My home page :: Multiple comparison

Pairwise comparison of phylogenies -- old version

This page provides access to my original applet for comparing pairs of alternative phylogenies described in a paper in Bioinformatics. The applet has been replaced with a newer version and this page is maintained only for reference.

Phylogeny A:
Phylogeny B:


The two phylogenies should be specified using the standard "bracket and comma" format for dendrograms. 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);

It's worth noting the following:

  • The dendrogram information must be terminated with a semicolon.
  • The dendrograms specified can be either rooted or unrooted ie. contain either a bifurcation or trifurcation at the top level.
  • It's best if the dendrograms contain the same set of leaf labels. However, the program can handle trees that do not share the complete set of labels: leaves present in one tree but missing in the other are shaded grey.
  • Comparison of trees containing hundreds of leaves will take several minutes. If you want to do this regularly it would probably be best to contact us for the stand-alone software.

If you have difficulty displaying the applet, it may be that your browser cannot display embedded Java or the browser is configured incorrectly. It is more reliable to obtain the complete source code from us and run it independently from a browser. Be warned: THIS APPLET MIGHT MAKE YOUR BROWSER CRASH.

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.