Windows 95/98/Me: copy quartet.exe to c:\windows\command
Windows NT/2000: copy quartet.exe to c:\winnt\system32
Windows XP: copy quartet.exe to c:\windows\system32
Linux binary: copy quartet to /usr/local/bin
You may need admin/root privileges to install the program to
these locations.
It is not necessary to install quartet to the system
directory; you can use it from any folder, but if it is not in the system
directory you will have to navigate to the folder that quartet is in before you
will be able to use it. Alternatively on windows you can add the location of
the program to the windows path environment variable.
All arguments must be entered with an equals sign between it
and its corresponding value, and no spaces in between. All argument value pairs
must be separated by spaces i.e.
quartet [argument]=[value] [argument1]=[value1]
Example:
quartet tree=test.tre log=log.txt algorithm=simple
tree=[filename]
specifies a file with one or more trees in newick format to use as the input set. Note that multiple trees arguments can be used so that multiple files can be loaded as the input set.
I.e. tree=file1.tre tree=file2.tre would load both files into the program as input data.
log=[filename]
Specifies the file to append program output to. If this argument is omitted the output is only shown on the console.
algorithm=[greedy or simple]
Specifies which algorithm to use when filling in missing taxa. If this argument us omitted then the simple algorithm is used by default
simple
This algorithm finds the first missing taxon from a tree then finds the best place for it (or given multiple optimal placements will pick a random optimal placement). This process is repeated until no more taxa are missing from the tree.
greedy
This algorithm searches through all missing taxa and finds the taxon which gives the highest quartet score (or a random pick between taxa that share the highest score). This taxon is then placed in the tree in the most optimal place in the tree. This then repeats for the next missing taxon with the highest score until no missing taxa remain. This algorithm is considerably slower than the simple algorithm.
output=[foldername]
Specifies the folder to output the completed input trees to. If this argument is omitted then the output trees will appear in the same directory as the input files.
The program outputs the completed trees as newick format tree files. It also outputs the trees in the same structure that they were input with each file including the prefix “completed_” in addition to the name of the original input file.
I.e. with the input tree=tree1.tre tree=tree2.tre the outputted tree files will be
completed_tree1.tre and completed_tree2.tre
Also note that branch length data on input files will be stripped from the output files.