Búsquedas heurísticas TNT

TNT is the best program available for performing heuristic searches with parsimony. The Willi Hennig Society has made it freely available since 2007. The download site was recently moved to Pablo Goloboff's institutional website.
Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15:415-428.
Goloboff P.A., Farris J.S., Nixon K.C. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774-786.
Nixon, K.C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414.
1. Execute TNT. (Mac users: go to directory where TNT is located and type "./tnt.command"; You may want to add this file to your PATH).
2. To see a list of available commands, type "help;" (PC users: if you don't see the command line at the bottom of the screen, you can activate it by selecting "File -> Command line").
3. To save results to a log file, type "log zilla.txt".
4. If you opened tnt from its original folder, the accompanying rbcL sequence alignment (zilla.tnt) is in the same place. To activate the file, type "proc zilla.tnt" at the command line. (If exporting another molecular sequence alignment from Mesquite, you will probably want to to select "convert gaps as missing").
5. To perform a heuristic search, explore the options available for the ratchet by typing "ratchet?";
6. Type:
randtrees 1;
ratchet = iter 50;
7. What is the length of the optimal tree(s)? How many times was it found? If you like, re-run the ratchet with more iterations.
8. Explore the options available for the xmult command by typing "xmu?".
9. Type "xmu = hit 20 drift 10;". What is the length of the optimal trees? How many times was the optimum tree found?
10. To see one of the resulting equally-most-parsimonious trees (Mac users will be able to see the tree better in the log file), type "tplot 0;". You can use the ESC button to return to the main screen.
11. To see the first MPT tree with branch lengths displayed, type "blength *0;".
12. To save trees type:
taxname= tsave *zilla-ex;
tsave /;
13. How many trees are in the file? Open the file in a text editor. Is it in Newick format?
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 the strict consensus tree, type "nelsen*;".
16. To display the consensus tree on the screen (and send it to the log file), type "tplot x;", where "x" is the tree number for the consensus indicated by TNT in the previous step.
17. Type "export * zilla.nex;". Open the file in FigTree. The file should include the MPT and the nelsen tree.
18. To perform a bootstrap, type "resample boot replications 100;".
19. To stop saving to log file, type "log /;".
20. To quit, type "zzz".