---
name: "primeDTLSR"
section: "1"
platform: "linux"
package: "prime-phylo"
version: "1.0.11-13+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/primeDTLSR"
---

# primeDTLSR(1)

Guest-in-host tree inference tool

## NAME

primeDTLSR - Guest-in-host tree inference tool

## SYNOPSIS

**primeDTLSR** \[*OPTIONS*\] *seqfile hostfile \[gsfile*\]

## DESCRIPTION

Guest-in-host tree inference enabling reconciliation analysis using the underlying DTLRS model. Model properties:

- 1\)

  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.

- 2\)

  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.

- 3\)

  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.*

## 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\|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 .

- **-Ef**

  Fix mean and variance of edge rate distribution. 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.

- **-Bp** ***FLOAT*** ***FLOAT*** ***FLOAT***

  Initial duplication, loss and transfer rates. Defaults to ,  and .

- **-Bf**

  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 conf\_value\_from\_cmake\_DiscMinIvs@.

- **-C** ***UNSIGNED\_INT***

  Number of transfer counts during sampling. Defaults to .

- **-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.

- **-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

[**primeDLRS**(1)](/primeDLRS/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)