Does anyone could share a protocol for divergence time calculation based on nucleotide sequences (plant chloroplast genomes)?
I tried with BEAST but failed to generate the input file xml file by BEAUti.
My potocol as follows;
BEAUTi (V. 1.8)
File-> Import input.nexus data
@taxa -> ingroup (only known samples: ex: rice & sorghum divergence time: 13mya ) and outgroup
@sites -> HYK (substitution model), Gamma (site heterogeneity model)
@clocks -> strict model
@trees -> yule process
@Prior-> All normal, tmrca (untitled)-> normal (Mean:13 SD; 2) how this value calculated?
Ucld.mean -> gamma -> shape: 1000, scale: 0.001,
@MCMC -> length of chain-1,000,000 generation, Echo state – 10,000, log parameter – 1000
5,000,000 generation, Echo state – 50,000, log parameter – 1000
The Error while generating xml file for BEAST
“ BEAST has terminated with an error. Please select QUIT from the menu.
Parsing error - poorly formed BEAST file, uTb_mfft_nexus 28+1_strict_pri17+2.xml:
Error parsing '' element with id, 'null':
Uniform prior uniformPrior cannot take a bound at infinity, because it returns 1/(high-low) = 1/inf
”
plz suggest me how to overcome this issue.
Any other protocol you like to suggest?
Many thanks
sam