mptp command line options

Below is a complete list of all command-line options of mptp, grouped by category.

General options:

Option	Description
--help	Display help menu and exit.
--version	Output version information and exit.
--quiet	Suppress all output to stdout except for warnings and fatal error messages.
--tree_file filename	Input newick file that contains a phylogenetic tree. Can be rooted or unrooted.
--output_file filename	Specifies the prefix used for generating output files. For ML species delimitation two files will be created. First, filename.txt that contains the actual delimitation and filename.svg that contains an SVG figure of the computed delimitation. For a single mcmc run, four files will be created. First, filename.run_seed.stats containing the credible interval for the number of species and the frequency for each species number. Then the files filename.run_seed.svg and the filename.run_seed.tree contain the newick tree with the support values for the each node being part of the speciation process. Finally the filename.run_seed.txt file contains information about the run and the ML delimitation. If the --mcmc_log option is used, two additional files will be generated the filename.run_seed.log and the filename.run_seed.logl.svg, which contain the likelihood values in a text format and a plot respectively.
--outgroup	comma-separated list of taxa. All computations for species delimitation are carried out on rooted trees. This option is used only (and is required) in case an unrooted tree was specified with the --tree_file option. mptp roots the unrooted tree by splitting the branch leading to the most recent common ancestor (MRCA) of the comma-separated list of taxa into two branches of equal size and introducing a new node (the root of the new rooted tree) that connects these two branches.
--outgroup_crop	Crops taxa specified with the --outgroup option from the the tree.
--minbr real	Any branch lengths in the input tree smaller than or equal to the value provided with this command are excluded (ignored) from the computations. In addition, for mcmc analyses, subtrees that exclusively consist of branch lengths smaller or equal to real are completely ignored from the proposals (support values for those clades are set to 0). (default: 0.0001)
--precision positive integer	Specifies the precision of the decimal part of floating point numbers on output (default: 7)
--minbr_auto FASTA_filename	Automatically detects the minimum branch length. For this option a fasta formated alignment should be provided. The method identifies the subtrees that consist of sequences with zero p-distances and returns the minimum branch length value that should then be used with the --min_br command for either a ML or an MCMC delimitation analysis.
--tree_show	Show an ASCII version of the processed input tree (i.e. after it is rooted by, potentially cropping, the outgroup).

Maximum-likelihood estimations:

Option	Description
--ml --single	Triggers the algorithm for computing an ML estimate of the delimitation using the PTP model.
--ml --multi	Triggers the algorithm for computing an ML estimate of the delimitation using the mPTP model.
--pvalue real	Only used with the PTP model (specified with --single). Sets the p-value for performing a likelihood ratio test (default: 0.001). Note that, there is no likelihood ratio test for the mPTP model.

MCMC method:

The MCMC method is triggered with the --mcmc switch combined with either --single (the PTP model) or --multi (the mPTP model).

Option	Description
--mcmc positive integer --single	Triggers the algorithm for computing support values by taking the specified number of MCMC samples (delimitations) using the PTP model.
--mcmc positive integer --multi	Triggers the algorithm for computing support values by taking the specified number of MCMC samples (delimitations) using the mPTP model.
--mcmc_sample positive integer	Sample only every n-th MCMC step.
--mcmc_log	Log the scores (log-likelihood) for each MCMC sample in a file and create an SVG plot.
--mcmc_burnin positive integer	Ignore all MCMC samples generated before the specified step. (default: 1)
--mcmc_runs positive integer	Perform multiple MCMC runs. If more than 1 run is specified, mptp will generate one seed for each run based on the provided seed using the --seed switch. Output files will be generated for each run (default: 1)
--mcmc_credible real	Specify the probability (0.0 to 1.0) for which to generate the credible interval i.e., the probability the true number of species will fall within the credible interval given the observed data. (default: 0.95)
--mcmc_startnull	Start MCMC sampling from the null-model (all branches fitting one exponential distribution).
--mcmc_startrandom	Start MCMC sampling from a random delimitation.
--mcmc_startrandom	Start MCMC sampling from the ML delimitation.
--seed positive integer	Specifies the seed for the pseudo-random number generator. (default: randomly generated based on system time)

SVG Output:

The ML method generates one SVG file that visualizes the processed input tree (i.e. after it is rooted by, potentially cropping, the outgroup) and marks the subtrees corresponding to coalescent processes (the detected species groups) with red color, while the speciation process is colored black.

The MCMC method generates one SVG file per run visualizing the processed tree, and indicates the support value for each node, i.e., the percentage of MCMC samples (delimitations) in which the particular node was part of the speciation process. A value of 1 means it was always in the speciation process while a value of 0 means it was always in a coalescent process. The tree branches are colored according to the support values of descendant nodes; a support of value of 0 is colored with red, 1 with black, and values in between are gradients of the two colors. Only support values above 0.5 are shown to avoid packed numbers in dense branching events. In addition, if --mcmc_log is specified, an additional SVG image of log-likelihoods plots for each sampled delimitation is created.

Option	Description
--svg_width positive integer	Sets the total width (including margins) of the SVG in pixels. (default: 1920)
--svg_fontsize positive integer	Size of font in SVG image. (default: 12)
--svg_tipspacing positive integer	Vertical space in pixels between taxa in SVG tree. (default: 20)
--svg_legend_ratio real	Ratio (value between 0.0 and 1.0) of total tree length to be displayed as legend line. (default: 0.1)
--svg_nolengend	Hide legend.
--svg_marginleft positive integer	Left margin in pixels. (default: 20)
--svg_marginright positive integer	Right margin in pixels. (default: 20)
--svg_margintop positive integer	Top margin in pixels. (default: 20)
--svg_marginbottom positive integer	Top margin in pixels. (default: 20)
--svg_inner_radius positive integer	Radius of inner nodes in pixels. (default: 0)