TNT instructions (MAC)

TNT Instructions for Mac

(comiled from http://phylobotanist.blogspot.com/2015/03/parsimony-analysis-in-tnt-using-command.html)

 

• Open TNT from the tnt.command file (opens in Terminal).

 

• First – Increase memory, e.g. to 2000 Mb

mxram 2000;

[Note that many commands need a semicolon at the end]

 

• Tell TNT to use taxon names in trees it saves:

taxname=;

 

• Then read in a tnt matrix:

procedure [drag & drop file to reveal its path]

 

NOTE: file path must not include any spaces or symbols like / or \

 

• Set the maximum number of most parsimonious trees, e.g. 1000 (default =100)

hold 1000

 

• Set your working directory (where your files will be saved)

cd [drag and drop folder]

• Create a text file of the session log:

log filename

 

• First do a simple, preliminary rapid search:

mult=replic 100;

[This generates 100 searches (random addition sequence searches) with both SPR and TBR]

 

• Then do a more thorough branch-swapping search using the trees found by mult:

bbreak=tbr;

 

• For a strict consensus of all the trees you have found, enter

nelsen *;

 

• If you want to save all trees (it also saves the data matrix and the consensus tree- figtree can open this):

export * alltrees.trees;

 

•  To save the consensus tree only, first choose it:

tchoose { strict } ;

 

• Enable tree tags (metadata):

ttags = ;

 

• Include branch length data with tree

blength *;

 

• View the tree:

ttags ;

 

• Save just the consensus tree with branch lengths:

export – consensus_tree.tre ;

[Note: TNT writes branch lengths in as labels inside the tree file – figtree can display these, but does not read them as branch lengths]

 

• Open the consensus_tree.tre file in Figtree. Note the node / branch label is simply a node number.

 

 

To perform a bootstrap analysis:

ttags = ;

collapse tbr ;

resample replications 100 ;

keep 1 ;

ttags ;

export – boots.tre;

 

• Open boots.tre in Figtree. Node / branch label is the bootstrap percentage.

• Don’t forget to check out the log file you created (called ‘filename’ by default)