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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
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citation info mixed with Alignment Filter info #209

Closed walterxie closed 7 years ago

walterxie commented 10 years ago

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A Ignoring ambiguities in tree likelihood. With 79 unique site patterns. Using rescaling scheme : dynamic Filter 2-457\3,660-896\3 12 taxa 231 sites 120 patterns Ignoring ambiguities in tree likelihood. With 120 unique site patterns. Using rescaling scheme : dynamic Filter 3-457\3,661-896\3 12 taxa 231 sites 82 patterns Ignoring ambiguities in tree likelihood. With 82 unique site patterns. Using rescaling scheme : dynamic Filter 4-457\3,662-.\3 12 taxa 231 sites 204 patterns Ignoring ambiguities in tree likelihood. With 204 unique site patterns. Using rescaling scheme : dynamic software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537

Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology 61(1):138-149.

Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174.

tgvaughan commented 10 years ago

Is this a race condition caused by multithreading?

alexeid commented 10 years ago

Are they both printed to the same stream? System.out and System.err are often interleaved.

On 28/08/2014, at 5:20 pm, Tim Vaughan notifications@github.com wrote:

Is this a race condition caused by multithreading?

— Reply to this email directly or view it on GitHub.

walterxie commented 10 years ago

it was single thread, and happened in trunk when you open BEAST as soon as you close one (red square button "stop" in Intellij).

alexeid commented 10 years ago

I believe that calls to System.err and System.out are internally handled by different threads and therefore not globally synced between the two, so they can interleave even if the calls were made from a single thread. All messages that are not errors should go to System.out - then they will appear in the correct order if they are called from the same thread.

On 29/08/2014, at 10:04 am, Walter notifications@github.com wrote:

it was single thread

— Reply to this email directly or view it on GitHub.

walterxie commented 7 years ago

This seems to be fixed in 2.4.6:

=============================================================================== Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537

Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174.

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