-
-
Notifications
You must be signed in to change notification settings - Fork 61
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
2567d0b
commit 2b76ab5
Showing
2 changed files
with
75 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| <phytime run.id="June2018" output.file="out" mcmc.chain.len="1E+7" mcmc.sample.every="100" | ||
| mcmc.print.every="50" mcmc.burnin="10000" mutmap="no" r.seed="1"> | ||
|
|
||
| <!-- Tree topology --> | ||
| <topology> | ||
| <instance id="T1" init.tree="bionj" optimise.tree="yes"/> | ||
| </topology> | ||
|
|
||
|
|
||
| <lineagerates model="lognormal"/> | ||
|
|
||
| <!-- Substitution model --> | ||
| <ratematrices id="RM1"> | ||
| <instance id="M1" model="HKY85" optimise.tstv="no" tstv="4.0"/> | ||
| </ratematrices> | ||
|
|
||
|
|
||
| <!-- Freerate model of variation of rates across sites --> | ||
| <siterates id="SR1"> | ||
| <instance id="R3" init.value="0.5"/> | ||
| <instance id="R2" init.value="1.0"/> | ||
| <instance id="R1" init.value="2.0"/> | ||
| <weights id="D1" family="freerates" optimise.freerates="no"> | ||
| <instance appliesto="R3" value="0.33"/> | ||
| <instance appliesto="R2" value="0.33"/> | ||
| <instance appliesto="R1" value="0.33"/> | ||
| </weights> | ||
| </siterates> | ||
|
|
||
| <!-- Nucleotide frequencies --> | ||
| <equfreqs id="EF1"> | ||
| <instance id="F1" optimise.freqs="no"/> | ||
| </equfreqs> | ||
|
|
||
|
|
||
| <!-- Vector of edge lengths --> | ||
| <branchlengths id="BL1" > | ||
| <instance id="L1" optimise.lens="no"/> | ||
| </branchlengths> | ||
|
|
||
| <!-- Model assembly --> | ||
| <partitionelem id="partition1" file.name="./seq.txt" data.type="nt" interleaved="no"> | ||
| <mixtureelem list="T1, T1, T1"/> | ||
| <mixtureelem list="M1, M1, M1"/> | ||
| <mixtureelem list="F1, F1, F1"/> | ||
| <mixtureelem list="R1, R2, R3"/> | ||
| <mixtureelem list="L1, L1, L1"/> | ||
| </partitionelem> | ||
|
|
||
|
|
||
| <clade id="CLADE1"> | ||
| <taxon value="Gymno_Cycas"/> | ||
| <taxon value="Gymno_Ginkgo"/> | ||
| <taxon value="Gymno_Juniperus"/> | ||
| </clade> | ||
| <calibration id="CAL1"> | ||
| <lower>290</lower> | ||
| <upper>452</upper> | ||
| <appliesto clade.id="CLADE1"> | ||
| </appliesto> | ||
| </calibration> | ||
| <clade id="CLADE2"> | ||
| <taxon value="Fagales_Juglans"/> | ||
| <taxon value="Ophioglossum"/> | ||
| </clade> | ||
| <calibration id="CAL2"> | ||
| <lower>0</lower> | ||
| <upper>10000</upper> | ||
| <appliesto clade.id="CLADE2"> | ||
| </appliesto> | ||
| </calibration> | ||
|
|
||
| </phytime> | ||
|
|
||
|
|
Empty file.