Commands/resample

From TNT

RESAMPLE
Version: 1.1.
Menu path: Analyze→Resample.

Resample
   Resample matrix, and calculate group supports. 
   Usage: "resample options [ search commands ];" 
   To save supports to file, use save *.
   Options are: 
      jak             use normal jacknifing (i.e. independent deletion) 
      sym             use symmetric resampling, with p(up)=p(del) 
      boot            use normal bootstrapping 
      poisson         use Poisson-modified bootstrapping 
      probability N   change probability for "jak" or "sym" 
      replications N  number of replications 
      cut N           cutoff frequency or support 
      slope           summarize results with frequency slopes 
      gc              summarize results with frequency differences 
      frequency       summarize results with absolute frequencies 
      from N          calculate support for groups in tree N 
      savetrees       save consensus for each replication 
      allow           during each replication, allow execution of 
                      (almost) all commands, including dangerous ones. 
                      This option should be used sparingly and only when 
                      you really know what you're doing! 
      zerowt          if doing symmetric resampling, eliminated (give 
                      weight 0) to downweighted characters (=default); 
                      otherwise, divide their weight by 2 (uncontra- 
                      dicted groups appear in all replicates) 
      sibyl           perform a backwards-jacknife; if used, this 
                      must precede all other arguments. See below 
                      for details. 
      errcount N      valid only under sibyl.  This counts the  
                      proportion of groups (out of the total 
                      supported groups) in the reduced data set 
                      that are not supported in the complete data 
                      set (wrong groups) and the proportion of groups 
                      (out of the total) in reference tree N (presu- 
                      mably, consensus of optimal trees for the 
                      complete data set) that are not supported by 
                      the reduced data set (mist groups). 

Taxa can be excluded from consensus calculations, using "/" followed  
by the list of taxa to exclude.  All options are persistent, except 
taxon exclusion and "from" 
    

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   The backwards jacknife is not a measure of support, but provides 
   instead a sort of stability test. It deletes characters (under 
   independent character removal, with p(del)=0.33); for each case, 
   runs the data (as indicated within square brackets) and count the 
   number of groups supported by the reduced data set that are present 
   in all previously existing trees ("supported") or present in some 
   but not all existing trees ("compatible").  Divide that number by 
   the total number of groups supported in the reduced data set, or by 
   the total number of groups that _could_ be supported in the reduced 
   data set (i.e. nr. of taxa-2 , "normalized"). The existing trees must 
   be provided by the user, and should correspond to a set of optimal 
   trees under current settings. Other than search commands, only the 
   number of replications can be changed, and taxa can be disregarded.

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Example: calculate bootstraping with 1000 replications excluding taxon2.

 taxon2 has placed in several positions in your equally parsimonious trees
and you want to calculate the boostrap values excluding it.

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Example: calculate jacknifing with 1000 with a probability of deletion of 0.75 for each character.