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Prerequisites

To try the following examples, first do the following:

  1. Download the data from examples.zip
  2. Unzip the downloaded file. After unzipping, you should see a folder named examples
  3. Change directory to examples
  cd examples

Use Case 1: Infer time-resolved branch lengths, heritable missing rate, and dropout rates of a fixed tree topology

LAML can infer time-resolved branch lengths and the rates of the two missing data types for a fixed tree topology. If the time frame of the experiment is specified by --timescale, the output tree will be scaled to the same height. Otherwise, the output tree will be scaled to the unit height 1.

For example, the following command:

run_laml -c examples/example1/character_matrix.csv -t examples/example1/starting.tree -p examples/example1/priors.csv -o example1 --nInitials 1 --timescale 10 -v

specifies the tree via -t and set --timescale to 10. Running this command will produce three output files

  1. example1_trees.nwk: the output tree containing time-resolved branch lengths. This tree has the same topology as the starting tree specified in -t, but has branch lengths in time units
  2. example1_params.txt: this file reports the dropout rate, silencing rate, the negative log-likelihood of the tree topology and parameters, and the mutation rate
  3. example1_annotations.txt: This file has two components (i) the newick string of the rooted tree with internal nodes labeled and branch lengths show the infer number of mutations. (ii) imputed sequences for each node in the tree. If a site has multiple possible states, it is annotated with the probability of each possible state.

We provide sample outputs in examples/out_example1/ for your reference.

Use Case 2: Infer tree topology, branch lengths, and missing data rates

LAML can simultaneously infer tree topology, branch lengths, and the missing data rates using the --topology_search option.

For example, the following command:

run_laml -c examples/example2/character_matrix.csv -t examples/example2/starting.tree -p examples/example2/priors.csv -o example2 --nInitials 1 --randomreps 1 --topology_search -v --timescale 10

enables topology search using the flag --topology_search.

Running this command will produce three output files

  1. example2_trees.nwk: the output tree with time-resolved branch lengths. Because topology search has been performed, this tree has a different topology from the starting tree. The new topology has higher likelihood than the starting tree.
  2. example2_params.txt: this file reports the dropout rate, silencing rate, the negative log-likelihood of the tree topology and parameters, and the mutation rate
  3. example2_annotations.txt: This file has two components (i) the newick string of the rooted tree with internal nodes labeled and branch lengths show the infer number of mutations. (ii) imputed sequences for each node in the tree. For sites with multiple possible states, that site is annotated with the probability of each possible state.

In addition, a checkpoint file example2._ckpt.<randomnumber>.txt is produced, which is important for running LAML on large data. Every 50 NNI iterations, this file is updated with a checkpoint containing (i) the NNI iteration number, (ii) the current best newick tree, (iii) the current best negative log-likelihood, (iv) the current best dropout rate, and (v) the current best silencing rate.

We provide sample outputs in examples/out_example2/ for your reference.