Demos

The demo programs are located in

./doc/code/demos/

They are intended to show some of the functionality of genesis in a ready-to-use setting. You can also use them as starting point for developing your own applications. Be however aware that the demos only contain basic error checks for the user input, for reasons of simplicity.

The simplest way to test and use them is to copy the needed files to the ./apps directory and compile them using make update. See Apps for setup instructions.

For the C++ demos, start by inspecting the main function. From there, all other functions of the demos are called.

Available demo programs

The following demo programs are available:

• Visualize Placements

  Takes one or more jplace file(s) and visualizes the distribution of Pqueries on the reference tree (that is, the number of placements per branch). For this, it uses color coding and outputs a Nexus file.

• Extract Clade Placements

  Takes a jplace file and a mapping of the taxa of its reference tree to some clade names. It outputs a jplace file for each clade, where each file contains all Pqueries that fell into that clade.

• Compare Jplace Files

  Takes two jplace files with the same reference tree and compares the placement of each Pquery. It outputs tables that show which and how Pqueries differ in their placement on the tree.

• Labelled Tree

  Takes a jplace file and optionally a Newick tree (for example, with additional bootstrap support values) and produces a Newick tree where each Placement is turned intoan individual branch on the original tree.

• Placement Histograms

  Takes a path to either a jplace file, or a directory containing jplace files, and builds histograms of the the placement mass (according to the like_weight_ratio, LWR) of each placement and of the Expected Distance between Placement Locations (EDPL).

See there for more details.