PAUPrat REST

PAUPrat

A tool to implement parsimony ratchet searches using PAUP.

toolId=PAUPRAT

Supported parameters

Relevant to  
Type
Default
Allowed values
Comment
All input.infile inputfile     this is the nexus file containing an aligned set of sequences to be analyzed
           
  Visible Parameter        
PAUPrat vparam.specify_nchar
Integer
none
all integers
this is the number of characters in the matrix. This is not yet checked for accuracy.
  vparam.specify_nreps
Integer
200
all integers
this specifies how many ratchet iterations
  vparam.specify_seed
Integer
0
all integers
when set to 0, this gives a random number generated by the code
  vparam.specify_pct
Integer
20
all integers
this sets what percentage of the data set to permute
  vparam.specify_mod
Integer
none
all integers
this sets an explicit number of characters to permute, specify_mod or specify_pct is required
  vparam.specify_wtmode
String
uniform
uniform, add,mult
Sets the weighting mode of the analysis
  vparam.specify_verbose
String
terse
verbose,terse
Adds or not comments in the output
  vparam.setup_increase
String
auto
auto,no
 
   
 
 
 
 
PAUP vparam.paup_branchalg
String
tbr
tbr,spr,nni
choose the PAUP branch swapping algorithm
  vparam.set_multrees
String
no
yes,no
for Pauprat this should always be no, so you might want to omit this paramter form your form so it always runs as default.
  vparam.set_rearrlimit
Integer
none
all integers
a value set here will restrict analysis to a certain number of rearrangments
  vparam.set_timelimt
Integer
none
all integers
 
  vparam.set_reconlimit
Integer
none
all integers
 
  vparam.set_maxtrees
Integer
none
all integers
only relevant when multrees=yes, so not relevant for PAUPrat
  vparam.set_autoincrease
String
no
no, auto
 
  vparam.set_increaseval
Integer
none
all integers
 
  vparam.set_outgroup
switch
0
0,1
user can elect of specify an outgroup
  vparam.set_outgroupb
String
none
all characters up to 256
user enters the outgroup string
   
 
 
 
 
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