--- name: "primeDLRS" section: "1" platform: "linux" package: "prime-phylo" version: "1.0.11-13+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/primeDLRS" --- # primeDLRS(1) Guest-in-host tree reconciliation tool ## 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 \-th iteration. Defaults to . - **-w** ***UNSIGNED\_INT*** Output diagnostics to stderr every \-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** \ \ 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 ## SEE ALSO [**primeDTLSR**(1)](/primeDTLSR/1.md), [**primeGEM**(1)](/primeGEM/1.md), [**showtree**(1)](/showtree/1.md), [**chainsaw**(1)](/chainsaw/1.md), [**reconcile**(1)](/reconcile/1.md), [**reroot**(1)](/reroot/1.md), [**tree2leafnames**(1)](/tree2leafnames/1.md), [**treesize**(1)](/treesize/1.md)