Overview of Command-line Parameters

Parameter	Explanation
--ml	Maximum-likelihood heuristic.
--multi	Use one lambda per coalescent (this is default).
--single	Use one lambda for all coalescent.
--pvalue REAL	Set p-value for LRT (default: 0.001)
--minbr REAL	Set minimum branch length (default: 0.0001)

Command line examples

The following command will execute a simple ML species delimitation inference, assuming a single coalescent rate averaged over all species.

$ mptp --tree_file tree_filename --output_file output_filename --ml --single --minbr 0.0009330519

Similarly, the following command will execute a simple ML species delimitation inference, assuming a different coalescent rate for each delimited species.

$ mptp --tree_file tree_filename --output_file output_filename --mcmc 1000000 --multi --minbr 0.0009330519

Output files

The execution of either of the above commands will create two output files. The output_filename.txt contains information about the run:

Command: mptp --tree_file RAxML_bestTree.filename --output_file test --ml --multi --minbr 0.0014909129 
Number of edges greater than minimum branch length: 234 / 364
Null-model score: 566.622329
Best score for multi coalescent rate: 566.622329
LRT computed p-value: -1.000000
LRT: passed
Number of delimited species: 36

Followed by the delimited species.

Species 1:
Sequence1
Sequence2
Sequence3
Sequence4

Species 2:
Sequence10
Sequence25
Sequence5
Sequence12

...
...
...

Example file for the output_filename.txt

The second output file output_filename.svg is a vector graphic of the phylogenetic tree that can be viewed with a browser (firefox, chrome etc) or any vector graphic software (Inkscape, Corel Draw etc.)..The ML delimitation scheme is illustrated in the graphic; with black are illustrated the branches of the speciation process and with red the branches of the coalescent process.

Example file for the output_filename.svg