Answers.Body: <p>The official <a href="http://www.beast2.org/increasing-esss/index.html" rel="nofollow noreferrer">BEAST</a> website suggests a number of solutions to improve the ESS of a parameter</p>
  
  <p>It is not uncommon to have <a href="https://www.ncbi.nlm.nih.gov/pubmed/27539485" rel="nofollow noreferrer">several billions of generations</a> so I don't imagine increasing your number of generations would hurt.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-25T12:40:18.560Z
Answers.LastActivityDate: 2018-04-25T12:40:18.560Z
Answers.UserDisplayName: cmdoret
Body: <p>Using starBeast I ran a 50 locus tree, with 34 individuals, using evolutionary models indicated by AICc in jModel test. I ran this tree with a MCMC chain length of 500 million, storing every 10,000 generations. I used a relaxed clock log normal. </p>
  
  <p>I get low ESS values for posterior, prior, birthRate.t:Species, YuleModel.t:Species, popMean, and TreeHeight.Species. 
  ucldMean.c:Locus_name is low for each loci. 
  The TreeHeight statisitcs also have low ESS values.
  Also rate.c:Locus_name.mean for each loci is low as well. </p>
  
  <p>Is there a way to change my parameters in Beauti to help increase the ESS values of these statistics? Is there a parameter that would likely cause the ESS values of these particular statistics to be low? Would increasing the MCMC chain length increase the ESS values, given that I've already run half a billion? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-17T07:26:40.603Z
Comments.Text: It is not my field, but I don't understand many abbreviations you use. You might get (more) answers if you explain with simpler words what is the problem. As I understand you want to increase the value of one value by optimizing some parameters of a program, is [this](https://groups.google.com/forum/#!topic/beast-users/jfoPtRpSbws) helpful? Is there something in the mailing list of the tool helpful? Did you try or read something to solve this?
Comments.UserDisplayName: llrs
Tags: <genomics><phylogenetics>
Title: How can I improve ESS values for ucldMean in beast?
ThreadText: # How can I improve ESS values for ucldMean in beast?
  
  (Asked by: username_0 on 2018-04-16)
  
  Using starBeast I ran a 50 locus tree, with 34 individuals, using evolutionary models indicated by AICc in jModel test. I ran this tree with a MCMC chain length of 500 million, storing every 10,000 generations. I used a relaxed clock log normal.
  
  I get low ESS values for posterior, prior, birthRate.t:Species, YuleModel.t:Species, popMean, and TreeHeight.Species.
  ucldMean.c:Locus\_name is low for each loci.
  The TreeHeight statisitcs also have low ESS values.
  Also rate.c:Locus\_name.mean for each loci is low as well.
  
  Is there a way to change my parameters in Beauti to help increase the ESS values of these statistics? Is there a parameter that would likely cause the ESS values of these particular statistics to be low? Would increasing the MCMC chain length increase the ESS values, given that I've already run half a billion?
  
  **Tags:** genomics, phylogenetics
  
  > **Comments:**
  > **username_1**: It is not my field, but I don't understand many abbreviations you use. You might get (more) answers if you explain with simpler words what is the problem. As I understand you want to increase the value of one value by optimizing some parameters of a program, is [this](https://groups.google.com/forum/#!topic/beast-users/jfoPtRpSbws) helpful? Is there something in the mailing list of the tool helpful? Did you try or read something to solve this?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-04-25. Score: 1
  
  The official [BEAST](http://www.beast2.org/increasing-esss/index.html) website suggests a number of solutions to improve the ESS of a parameter
  
  It is not uncommon to have [several billions of generations](https://www.ncbi.nlm.nih.gov/pubmed/27539485) so I don't imagine increasing your number of generations would hurt.
  
  
  ---
  
  