Command line interface¶

tsdate provides a Command Line Interface to access the basic functionality of the Python API.

$ tsdate

or

$ python3 -m tsdate

The second command is useful when multiple versions of Python are installed or if the tsdate executable is not installed on your path.

Argument details¶

This is the command line interface for tsdate, a tool to date tree sequences.

usage: tsdate [-h] [-V] {date,preprocess} ...

Positional Arguments¶

subcommand

Possible choices: date, preprocess

Named Arguments¶

-V, --version

show program’s version number and exit

Sub-commands:¶

date¶

Takes an inferred tree sequence topology and returns a dated tree sequence.

tsdate date [-h] [-m MUTATION_RATE] [-r RECOMBINATION_RATE] [-e EPSILON]
            [-t NUM_THREADS] [--probability-space PROBABILITY_SPACE]
            [--method METHOD] [--ignore-oldest] [-p] [-v VERBOSITY]
            tree_sequence output Ne

Positional Arguments¶

`tree_sequence`	The path and name of the input tree sequence from which we estimate node ages.
`output`	The path and name of output file where the dated tree sequence will saved.
`Ne`	estimated effective (diploid) population size.

Named Arguments¶

`-m, --mutation-rate`
	The estimated mutation rate per unit of genome per generation. If provided, the dating algorithm will use a mutation rate clock to help estimate node dates. Default: None
`-r, --recombination-rate`
	The estimated recombination rate per unit of genome per generation. If provided, the dating algorithm will use a recombination rate clock to help estimate node dates. Default: None
`-e, --epsilon`	Specify minimum distance separating time points. Also specifies the error factor in time difference calculations. Default: 1e-6
`-t, --num-threads`
	The number of threads to use. A simpler unthreaded algorithm is used unless this is >= 1. Default: None
`--probability-space`
	Should the internal algorithm save probabilities in ‘logarithmic’ (slower, less liable to to overflow) or ‘linear’ space (faster, may overflow). Default: ‘logarithmic’
`--method`	Specify which estimation method to use: can be ‘inside_outside’ (empirically better, theoretically problematic) or ‘maximization’ (worse empirically, especially with a gamma approximated prior, but theoretically robust). Default: ‘inside_outside’
`--ignore-oldest`
	Ignore the oldest node in the tree sequence, which is often of low quality when using empirical data.
`-p, --progress`	Show progress bar.
`-v, --verbosity`
	How much verbosity to output.

preprocess¶

Remove regions without data from an input tree sequence.

tsdate preprocess [-h] [--minimum_gap MINIMUM_GAP]
                  [--trim-telomeres TRIM_TELOMERES] [-v VERBOSITY]
                  tree_sequence output

Positional Arguments¶

`tree_sequence`	The tree sequence to preprocess.
`output`	The path and name of output file where the preprocessed tree sequence will saved.

Named Arguments¶

`--minimum_gap`	The minimum gap between sites to trim from the tree sequence. Default: ‘1000000’
`--trim-telomeres`
	Should all material before the first site and after the last site be trimmed, regardless of the length of these regions. Default: ‘True’
`-v, --verbosity`
	How much verbosity to output.