|primeDLRS(1)||General Commands Manual||primeDLRS(1)|
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.
- the guest tree topology and its divergence times are modelled with a duplication-loss process in accordance with the Gene Evolution Model (GEM).
- sequence evolution is modelled with a user-defined substitution model.
- sequence evolution rate variation over guest tree edges (relaxed molecular clock) are modelled with iid values from a user-selected distribution.
- 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.
- -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 .
- 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.
- Fix mean and variance of sequence evolution rate. Non-fixed by default.
- -Gi FILE
- Filename with initial guest tree topology.
- Fix initial guest tree topology, i.e. perform no branch-swapping. Non-fixed by default.
- 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 .
- 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
- 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.
- Do not print elapsed wall time and CPU time
- Do not print the command line
- Show misc. info to stderr before iterating. Not shown by default.
- Successful program execution.
- Some error occurred
- The prime-phylo home page: http://prime.sbc.su.se
SEE ALSO¶primeDTLSR(1), primeGEM(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)
|13 Mar, 2012||prime-phylo 1.0.11|