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PoMo-help.txt
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PoMo-help.txt
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usage: PoMo [-h] [-m {0,1}] [-u MM] [-s SM] [-g GM] [-f GS] [-d DS_RATIO]
[-t THETA] [-v] [--version]
hyphy_bin file
PoMo10 script version 1.0.2
positional arguments:
hyphy_bin Path of the HYPHY binary used to maximize the
likelihood.
file Name of the counts or fasta file containing the
alignment. Each individual's name must be "species-n"
where "species" is the name of its species, and "n" is
a number identifying the individual among the other
samples of the same population/species (it actually
does not matter which number is given to which
individual). No gaps or Ns are allowed, which means,
you have to remove columns where one of the
individuals has missing characters or unknowns. It
does not matter from which individual each base comes,
so you can sub-sample and randomly assign to
individuals within a species.
optional arguments:
-h, --help show this help message and exit
-m {0,1}, --molecular-clock {0,1}
Determines if you want the molecular clock constraint
(and therefore also look for a root) or not. Default
is yes. Type `-m 0` to specify no molecular clock.
-u MM, --MM MM Allows to choose a mutation model different from the
HKY (default option). `GTR` corresponds to the general
time reversible, `F81` to the Felsenstein 1981
(reversible, equal mutation rates), and `NONREV` to
the general nonreversible model (all substitution
rates are independent). To change, type for example
`--MM GTR`.
-s SM, --SM SM Allows to choose fixation rates. `-s NoSel`: fixation
rates are equal for all nucleotides; default. `-s
GCvsAT`: one parameter describes fixation difference
of GC versus AT, as is expected from biased gene
conversion. `-s AllNuc`: each nucleotide has a
different fitness (3 free parameters since only
fitness differences matter). Warning: estimating
fixation biases will be more time consuming.
-g GM, --GM GM Allows to set a variable mutation rate over sites,
gamma-distributed, approximated with a number of
classes as specified by the user. Default: uniform
mutation rate. For example, `--GM 6` specifies a gamma
distribution of total mutation rate with 6 discrete
categories.
-f GS, --GS GS Allows to set a variable fixation bias over sites,
gamma-distributed, approximated with a number of
classes as specified by the user. Default: uniform
fixation rate (`f 0`).
-d DS_RATIO, --ds-ratio DS_RATIO
Determines which proportion of the data is kept after
downsampling. Downsampling is done when sites do not
have the same coverage along the genome. In such a
case, all sites with coverage higher than a certain
sample size are downsampled, those with lower coverage
are discarded. The threshold sample size is chosen as
the highest possible that leaves the kept number of
sites above the specified threshold. By default,
sample sizes are decreased until at least 2 thirds of
the sites are included (`-d 0.66`).
-t THETA, --theta THETA
Manually set population diversity theta. This value
can only be set, if all species have a sample size of
1. If no value is specified, PoMo will ask the user
for theta on the command line if necessary.
-v, --verbose turn on verbosity (-v or -vv)
--version show program's version number and exit