## table of contents

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.

- 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 <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.

# EXIT STATUS¶

**0**- Successful program execution.
**1**- Some error occurred

# URL¶

# 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 |