Update README.md

README.md

@@ -69,6 +69,9 @@ There are four output files:
 3. `LAML_output_annotations.txt`: This file contains the inferred maximum likelihood sequences for all internal nodes and leaf nodes, with possible characters and associated probabilities for sites with more than one possibility.
 4. `LAML_output.log`: The LAML logfile.
 
+## Examples
+We provide two examples for the two common use cases of LAML. See [Examples.md](https://github.com/raphael-group/laml/tree/master/examples.zip) for more dtails.
+
 ## Advanced I/O options
 LAML has the following additional options for I/O
 ```
@@ -78,6 +81,7 @@ input options:
     -p PRIORS, --priors PRIORS    The input prior matrix Q. Default: if not specified, use a uniform prior.
 output options:
     -o OUTPUT, --output OUTPUT    Output prefix. Default: LAML_output
+    -v, --verbose         Show verbose messages.
 ```
 
 ### Customize the format of the input character matrix 
@@ -94,53 +98,8 @@ by default. However, if possible we highly recommend specifying mutation prior u
 
 **Not recommended** We also accept [Python-pickled files](https://docs.python.org/3/library/pickle.html#data-stream-format), as this is the indel prior output format for [Cassiopeia](https://cassiopeia-lineage.readthedocs.io/en/latest/notebooks/reconstruct.html). We print a warning if the keys of the pickled prior dictionary do not match the site names in your provided character matrix file. 
 
-### The output prefix
-The user can change the output prefix using `-o`. The default prefix is `LAML_output`.
-
-## Examples
-To try the following examples, first do the followings:
-1. Download the data from [examples.zip](https://github.com/raphael-group/laml/tree/master/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 and heritable missing and dropout rates on a fixed 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
-```
-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. 
+### The output prefix and verbose option
+The user can change the output prefix using `-o`. The default prefix is `LAML_output`. The software can be run in verbose mode using `-v`.
 
 ## Other options
 Below are some other important options available in LAML. For full documentation, please run `run_laml -h`.
@@ -163,7 +122,3 @@ Below are some other important options available in LAML. For full documentation
   --randomreps RANDOMREPS    Number of replicates to run for the random strategy of topology search.
   --maxIters MAXITERS   Maximum number of iterations to run topology search.
 ```
-### Other options
-```
-  -v, --verbose         Show verbose messages.
-```