This is the command primeGSRf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
primeDLRS, primeGSRf - Guest-in-host tree reconciliation tool
SYNOPSIS
primeDLRS [OPTIONS] seqfile hostfile [gsfile]
DESCRIPTION
Guest-in-host tree reconciliation tool, enabling analysis of e.g. guest tree topologies,
reconciliation properties and duplication-loss rates. Based on a Bayesian MCMC framework
using the underlying GSR model. The old program name, primeGSRf, is still available as a
symlink to primeDLRS.
1) the guest tree topology and its divergence times are modelled with a duplication-
loss process in accordance with the Gene Evolution Model (GEM).
2) sequence evolution is modelled with a user-defined substitution model.
3) sequence evolution rate variation over guest tree edges (relaxed molecular clock)
are modelled with iid values from a user-selected distribution.
4) sequence evolution rate variation over sites (positions) are modelled according to
a discretized Gamma distribution.
The implementation uses a discretization of the host tree to perform its computations.
Please review available options, as you will need to change default settings. Option -r
may be useful to avoid numeric issues due to scaling.
seqfile is a file with aligned sequences for guest tree leaves.
hostfile is a PrIME Newick file with host tree incl. divergence times. Leaves must have
time 0 and root have time > 0.
gsfile is a tab-delimited file relating guest tree leaves to host tree leaves if info not
included in hostfile.
OPTIONS
-h, -u, -?
Display help (this text).
-o FILE
Output filename. Defaults to stderr.
-s UNSIGNED_INT
Seed for pseudo-random number generator. Defaults to random seed.
-i UNSIGNED_INT
Number of iterations. Defaults to .
-t UNSIGNED_INT
Thinning, i.e. sample every <value>-th iteration. Defaults to .
-w UNSIGNED_INT
Output diagnostics to stderr every <value>-th sample. Defaults to .
-q Do not output diagnostics. Non-quiet by default.
-m MCMC|PDHC|PD
Execution type (MCMC, posterior density hill-climbing from initial values, or just
initial posterior density). Defaults to .
-Sm UniformAA|JC69|F81|JTT|UniformCodon|ArveCodon
Substitution model. by default.
-Su DNA|AminoAcid|Codon <Pi=float1 float2 ... floatn> <R=float1 float2
...float(n*(n-1)/2)>
User-defined substitution model. The size of Pi and R must fit data type (DNA: n=4,
AminoAcid: n=20, Codon: n=62). R is given as a flattened upper triangular matrix.
Don't use both option -Su and -Sm.
-Sn UNSIGNED_INT
Number of steps of discretized Gamma-distribution for sequence evolution rate
variation over sites. Defaults to (no variation).
-Ed Gamma|InvG|LogN|Uniform
Distribution for iid sequence evolution rate variation over guest tree edges.
Defaults to (not to confuse with -Sn).
-Ep FLOAT FLOAT
Initial mean and variance of sequence evolution rate. Defaults to simple rule-of-
thumb based on host tree times.
-Ef Fix mean and variance of sequence evolution rate. Non-fixed by default.
-Gi FILE
Filename with initial guest tree topology.
-Gg Fix initial guest tree topology, i.e. perform no branch-swapping. Non-fixed by
default.
-Gl Fix initial guest tree edge lengths (in addition to topology), i.e. fix the edge
lengths. Non-fixed by default.
-Bp FLOAT FLOAT
Initial duplication and loss rates. Defaults to and .
-Bf Fix initial duplication and loss rates. Non-fixed by default.
-Bt FLOAT
Override time span of edge above root in host tree. If the value is <=0, the span
will be set to equal the root-to-leaf time. Defaults to value in host tree file.
See also option -Dtt.
-Dt FLOAT
Approximate discretization timestep. Set to 0 to divide every edge in equally many
parts (see -Di). Defaults to . See -Dtt for edge above root.
-Di UNSIGNED_INT
Minimum number of parts to slice each edge in. If -Dt is set to 0, this becomes the
exact number of parts. Minimum 2. Defaults to . See -Dtt for edge above root.
-Dtt UNSIGNED_INT
Override number of discretization points for edge above root in host tree. By
default, irrespective of time span, this is set to the number of points for a
(hypothetical) root-to-leaf edge
-r Rescale the host tree so that the root-to-leaf time equals 1.0. All inferred
parameters will refer to the new scale. Off by default. Note that discretization
parameters are NOT rescaled.
-Z Do not print elapsed wall time and CPU time
-W Do not print the command line
-debuginfo
Show misc. info to stderr before iterating. Not shown by default.
EXIT STATUS
0 Successful program execution.
1 Some error occurred
URL
The prime-phylo home page: http://prime.sbc.su.se
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