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Difference between revisions of "Mothur v.1.7.0"

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(New page: * get.listcount command - Ever wonder after a cluster what sequences are in those bins?? Thanks to a user request, here is the solution. Given a list file, this command will output a ....)
 
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*[[hcluster]] command - clusters distance files of any size.  It's slower than the [[cluster]] command, which stores the distance in RAM to increase performance, so if you can fit your file in RAM use [[cluster]].
 
*[[hcluster]] command - clusters distance files of any size.  It's slower than the [[cluster]] command, which stores the distance in RAM to increase performance, so if you can fit your file in RAM use [[cluster]].
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* added all parameter to the [[summary.shared]] and [[collect.shared]] commands.  The sharedchao and sharedsobs calculators not only give you the pairwise richness estimates for your groups, but also estimate the combined richness of all your groups.  The all parameter allows you to specify whether or not you want mothur to find this combined group estimate.  By default it is set to true, but if you have a large number of groups the combined estimate may cause you to run out of ram, to avoid this problem and yet still get the pairwise richness estimates set all to false.

Revision as of 12:25, 10 November 2009

  • get.listcount command - Ever wonder after a cluster what sequences are in those bins?? Thanks to a user request, here is the solution. Given a list file, this command will output a .otu file for each distance specified containing the bin number and a list of the sequences in that bin.
  • updated read.otu command - you can now use the groups parameter to specify which groups you would like to use. If you provide groups mothur will generate a .rabund file for each group, a .shared file containing only those groups and a new group file containing only the sequences in the groups you specified.
  • hcluster command - clusters distance files of any size. It's slower than the cluster command, which stores the distance in RAM to increase performance, so if you can fit your file in RAM use cluster.
  • added all parameter to the summary.shared and collect.shared commands. The sharedchao and sharedsobs calculators not only give you the pairwise richness estimates for your groups, but also estimate the combined richness of all your groups. The all parameter allows you to specify whether or not you want mothur to find this combined group estimate. By default it is set to true, but if you have a large number of groups the combined estimate may cause you to run out of ram, to avoid this problem and yet still get the pairwise richness estimates set all to false.