kSNP / Discussion / General Discussion: Running kSNP with -ML and -min

Running kSNP with -ML and -min_frac commands

Cristina Kraemer Zimpel - 2018-03-05

Hi,
I am running kSNP with with the parameters of "-ML" and "-min_frac 0.75", and my doubt is related about this minimum fraction of genomes.
The maximum likelihood output trees with be constructed with the amount genomes that I have selected (75%)? Our the min_frac command will run just for parsimony trees?

As outputs I have:
tree_AlleleCounts.majority0.75.NodeLabel.tre
tree_AlleleCounts.majority0.75.tre
tree_AlleleCounts.ML.NodeLabel.tre
tree_AlleleCounts.ML.tre
tree_AlleleCounts.parsimony.NodeLabel.tre
tree_AlleleCounts.parsimony.tre
tree_tipAlleleCounts.majority0.75.tre
tree_tipAlleleCounts.ML.tre
tree_tipAlleleCounts.parsimony.tre
tree.majority0.75.tre
tree.ML.tre
tree.parsimony.tre

Thank you,
Cristina

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- Barry G. Hall - 2018-03-05
  
  Min_frac will run just for the parsimony tree. All the trees in your outputs that include majority0.75 are parsimony trees.
  
  Barry G. Hall
  
  On Mar 5, 2018, at 4:22 AM, Cristina Kraemer Zimpel criskzimpel@users.sourceforge.net wrote:
  
  Hi,
  I am running kSNP with with the parameters of "-ML" and "-min_frac 0.75", and my doubt is related about this minimum fraction of genomes.
  The maximum likelihood output trees with be constructed with the amount genomes that I have selected (75%)? Our the min_frac command will run just for parsimony trees?
  
  As outputs I have:
  tree_AlleleCounts.majority0.75.NodeLabel.tre
  tree_AlleleCounts.majority0.75.tre
  tree_AlleleCounts.ML.NodeLabel.tre
  tree_AlleleCounts.ML.tre
  tree_AlleleCounts.parsimony.NodeLabel.tre
  tree_AlleleCounts.parsimony.tre
  tree_tipAlleleCounts.majority0.75.tre
  tree_tipAlleleCounts.ML.tre
  tree_tipAlleleCounts.parsimony.tre
  tree.majority0.75.tre
  tree.ML.tre
  tree.parsimony.tre
  
  Thank you,
  Cristina
  
  Running kSNP with -ML and -min_frac commands https://sourceforge.net/p/ksnp/discussion/general/thread/77bc2b81/?limit=25#1a3c
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Running kSNP with -ML and -min_frac commands

kSNP4 does SNP discovery and SNP annotation from whole genomes

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Running kSNP with -ML and -min_frac commands

Running kSNP with -ML and -min_frac commands

kSNP4 does SNP discovery and SNP annotation from whole genomes

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Running kSNP with -ML and -min_frac commands