Provided by: prime-phylo_1.0.11-4build2_amd64
primeDLRS, primeGSRf - Guest-in-host tree reconciliation tool
primeDLRS [OPTIONS] seqfile hostfile [gsfile]
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.
-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.
0 Successful program execution. 1 Some error occurred
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primeDTLSR(1), primeGEM(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)