Description This example demonstrates how to use a data set, consisting of several partitions with potentially different models and even data types to jointly construct a phylogeny. Load and set up an example data set. We shall use a small data set consisting of two introns and an exon as an example. The data file is NEXUS format and includes some partitioning information in an ASSUMPTION block. The example file can be obtained here. Save this example file on your hard drive, open it in HyPhy, using File:Open:Open Data File, then change the data type of the 'Exon' partition to 'Codon' and its model - to MG94xHKY85_3x4 with 'Global' parameter option, while setting the model for the intron to HKY85 with 'Global' options. For basic instructions on how to work with data partitions refer to this example. Select 'Infer Tree' under 'Tree Topology' for both partitions. The data panel should now look like this: Note the orange light in the status bar: HyPhy is now ready to start the analysis. Run the reconstruction Choose 'Likelihood:Inference:Infer Topology' menu options. A dialog box, prompting you to select a search strategy, is shown. Since our data set contains only 5 sequences, we can try all possible trees (there are 15), thus we choose 'Exhaustive_Search'. For larger trees, 'Sequential_Addition' with branch swapping is more feasible. HyPhy will examine all 15 possible trees, jointly estimating model parameters for both partitions and select the best one. Once the estimation process has concluded, the trees are automatically assigned to every partition which participated in the inference, and set parameter values to their MLEs. You may view the results by invoking 'Likelihood:Show Parameters'. Refer to this example for pointers on how to work with the parameter table. Further pointers You can define custom substitution models (see this example) to use in reconstruction, and also perform constrained searches, e.g. by sharing some of the parameters between partitions, reconstructing the trees under molecular clock etc. An example of this functionality is under development, but feel free to expreiment with 'Infer Topology with Constraints' option.