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I wouldn't, to be honest, not that it's not a great hardwood, just you don't get the length of burn you do with seasoned ash, oak when we can get it.
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We run the program using a length of burn-in Period of 100 000 and 10 0000 repetitions of MCMC after burning.
The software was set to have length of burn-in period of 500,000 followed by 500,000 Markov chain Monte Carlo (MCMC) reps after burn-in.
The length of burn-in Markov Chain Monte Carlo (MCMC) replications was set to 10000 and data were collected over 100000 MCMC replications in run, based on previous literature suggesting that this level is sufficient (Evanno et al. 2005).
The length of burn-in time and replication number were both set to 100,000 in each run.
Thus, when running multiple chains, each with a significant length of burn-in, the speedup does not scale well with the number of available CPU cores.
We selected the length of burn-in and the number of MCMC (Markov Chain Monte Carlo) replications after burn-in both to be 50,000.
STRUCTURE runs were carried out with a length of burn-in and MCMC (Markov chain Monte Carlo) of 100,000 each.
AWTY system [ 36] was used to assess the length of MCMC run and Tracer v. 1.4.1 [ 37] was used to ascertain the length of burn-in periods.
Length of burn-in of the Markov Chain Monte Carlo (MCMC) iterations was set to 100,000, and data were collected over 100,000 MCMC iterations in each run.
Parameters for multipoint estimation of recombination frequency were generally increased (length of burn-in chain, from 10,000 to 20,000; number of Monte Carlo EM cycles, from 4 to 10; chain length per EM cycles, from 1000 to 5000) to ensure convergence.
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