--help

Display help text 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 maximum-likelihood 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 mcmc analyses, a file filename.txt is created that contains the newick tree with supports values.

--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.

--min_br real

Any branch lengths in the input tree smaller or equal than real 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 filename

Automatically detects the minimum branch length from the p-distances of the FASTA file filename.

--tree_show

Show an ASCII version of the processed input tree (i.e. after it is rooted by, potentially cropping, the outgroup).

Estimating the maximum-likelihood delimitation is triggered by the switch --ml followed by --single (the PTP model) or --ml --multi (the mPTP model). Note that these two methods affect how options --output_file behaves and can be controlled using the --min_br switch. Both methods require a rooted phylogenetic tree, however an unrooted tree may be specified in conjunction with the option --outgroup. In this case, mptp roots it at that outgroup (see General options, --outgroup for more info). Note that both methods output an SVG depiction of the ML delimitation. See Visualization for more information on adjusting and fine-tuning the SVG output.

Both methods ignore discard branch lengths of size smaller than the size specified using the --min_br option. The PTP model then attempts to find a connected subgraph of the rooted tree that (a) contains the root, and (b) the sum of likelihoods of fitting the edges of that subgraph in one exponential distribution and the remaining edges in another (exponential distribution) is maximized. With likelihood we mean the sums of the probability density function with the mean defined as the reciprocal of the average of edge lengths in the particular distribution.

--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. Note that, there is no likelihood ratio test for the mPTP model this test is not done. (default: 0.001)

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

Some more stuff to write

--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.

--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)

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 green.

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.

--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)