SYNOPSISprimeDTLSR [OPTIONS] seqfile hostfile [gsfile]
Guest-in-host tree inference enabling reconciliation analysis
using the underlying DTLRS model. Model properties:
- The guest tree topology evolves inside the host tree by means of duplication, loss and horizontal transfer events guided by homogeneous rates, much like a birth-death process. Lineages branch deterministically at host tree nodes.
- Relaxed molecular clock; sequence evolution rate variation over guest tree edges. Rates are drawn iid from specified distribution. Also, rate variation over sites may be added, using discretized gamma distribution with mean 1.
- Substitution model of choice; standard or user-defined. The implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state.
The implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state.
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|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 rate variation among edges. Defaults to .
- -Ep FLOAT FLOAT
Initial mean and variance of edge rate distribution. Defaults to and .
- Fix mean and variance of edge rate distribution. 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.
- -Bp FLOAT FLOAT FLOAT
- Initial duplication, loss and transfer rates. Defaults to , and .
- Fix duplication, loss and transfer rates to initial values. Non-fixed by default.
- -Bt FLOAT
- Override time span of edge above root in host tree. Must be greater than 0. Defaults to file-contained value.
- -Dt FLOAT
- Approximate discretization timestep. Set to 0 to divide edge generations into the same amount of parts (see -Di). Defaults to .
- -Di UNSIGNED_INT
- Minimum number of discretization subintervals per edge generation. If -Dt is set 0, this becomes the exact number of subintervals. Minimum 2. @Defaults to [email protected]
- -C UNSIGNED_INT
- Number of transfer counts during sampling. Defaults to .
- 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.
- 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.
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- The prime-phylo home page: http://prime.sbc.su.se