PISH (Phylogenetic Inference SHell)

Reading from tnt.run 
Running tnt.run with arguments: input.fasta output.txt 
 
Screen size is 100 x 100 
TNT Version  1.1  May, 2008
Copyright (c) 1999 - 2001
P. A. Goloboff, James S. Farris, and Kevin C. Nixon
	
Run Phylogeny.fr script version 0.5
	
Record search status: none 
Macro language is ON 
Macros: 50.5 Kb in use, 51.8 Kb free
TNT - max. ram =  64.00 Mbytes 
No ram used yet 
	
	
Initialize parameters...
Random seed is 9335 
-sequences type (1)
Matrices will be read as DNA data 
Matrix space: allocate for up to 8 states 
Reading states as DNA 
Gaps will be read as fifth state 
sequences type set to DNA/RNA
-resampling (0)
...done!
	
Read input data...
Reading from input.fasta 
Again reading from tnt.run 
Matrix (7x9, 8 states). Memory required for data:   0.02 Mbytes 
...done!
Set substitution model (transition step/transversion step = 1)...
Using nucleic acid step matrix based on a transition step / transversion step ratio of 1
...done!
Computing...
-using New Technology search
sectorial search enabled
tree fusing enabled
Completed search.
Total rearrangements examined: 2,340. 
No target score defined.  Best score hit 1 times.
Best score: 7.  1 trees retained. 
...done!
Output data...
Log file: output.txt 
Tread 'set of 1 trees' 
(Pan_troglodytes (Australopithecus_africanus ((Paranthropus_Austr_boisei Paranthropus_Austr_aethiop
 
Tree file: output.txt 
Closing output.txt (with 0 trees saved)
 
Note: for consensus calculation, trees will be 
temporarily collapsed (when min. branch length = 0) 
Strict consensus of 1 trees (0 taxa excluded) calculated, as tree 1 
 
Note: for consensus calculation, trees will be 
temporarily collapsed (when min. branch length = 0) 
 
Strict consensus of 2 trees (0 taxa excluded) 
   ,-- Pan_troglodytes
   |  ,-- Australopithecus_africanus
|--|  |     ,-- Paranthropus_Austr_aethiopicus
   `--|  ,----- Paranthropus_Austr_boisei
      |  |  ,-- Homo_erectus
      `--|  |-- Homo_habilis
         `--|  ,-- Homo_heidelbergensis
            `--|  ,-- Homo_sapiens_sapiens
               `----- Homo_sapiens_neanderthalensis
Log file: output.txt 
Tread 'set of 1 trees' 
(Pan_troglodytes (Australopithecus_africanus ((Paranthropus_Austr_boisei Paranthropus_Austr_aethiop
 
 
Tree 0, min. branch lengths 
 
             0      1      2      3      4      5      6      7      8      9 
                                                                              
      0      0      0      0      0      0      0      0      0      0     -- 
     10      0      2      1      0      1      1      2 
 
 
Informative characters 
 
             0      1      2      3      4      5      6 
                                                         
      0     X      X      X      X      X      X      X  
 
 
Nexus output:
export DNA/RNA alignment and trees into Nexus format
Saved data and trees (Nexus format) to file tnt.nexus 
...done!