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Goloboff P.A., Farris J.S., Nixon K.C. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774-786.
1. Download "primates.nex", and move it to your "Phylogenetics" folder.
2. Open the file in Mesquite.
3. Export the file to your the same folder where you have your TNT executable file ("primates.tnt"), being sure to activate "convert gaps to missing".
4. Execute TNT. (Mac users: go to directory where TNT is located and type "./tnt.command".
5. To see a list of available commands, type "help;"
6. To save results to a log file, type "log primates.txt".
7. Activate the file (Mac users: type "proc primates.tnt").
8. To perform a branch-and-bound/implicit enumeration search, explore the options available for the ienum command by typing "ienum?". Then type "ienum;"
9. To see the resulting equally-most-parsimonious trees, type "tplot 0;" then "tplot 1;".
10. To see the first MPT tree with branch lengths displayed, type "blength *0;".
11. To save trees, type:
tsave *primates;
tsave /;
12. How many trees were saved? Open the file in a text editor. Is it in Newick format?
13. Now type "export * primatesALL.nex;". Examine the file in a text editor.
14. To get the consistency index and retention index, you can run a script. Copy the file "STATS.RUN" to the same directory as the tnt executable and type "proc STATS.RUN".
15. To calculate nelsen tree, type "nelsen*;".
16. To display the nelsen file on the screen, type "tplot 2;".
17. Type "export * primatesALL.nex;". Open the file in FigTree. The file should include the MPT and the nelsen tree.
18. To stop saving to log file, type "log /;".
19. To quit, type "zzz".
20. Read the TNT help page to learn more about how to use TnT.