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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
|
||
|
|
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|||
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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