Sometimes, it is useful to archive phylogenetics tips, tricks, and help. The overall organizational page for this will be phyloHelp. The owner/admin is me, Nicholas J. Matzke. My original purpose for such a page was to archive my own tips/tricks/help so that I could find them later through google, but I am happy to give accounts to others in phylogenetics who would like to use the page.
This page is devoted to TNT (Tree analysis using New Technologies), a parsimony program that is famous for being very fast, but for having a very obscure command syntax. TNT-related help should be put here, or linked from here.
See especially: TNTR (R functions and TNT scripts for common tasks), TNTwiki, and tnt.htm
Scraps of the old TNT wiki
The major source of help that used to exist for TNT was: http://tnt.insectmuseum.org/index.php/Main_Page . It has apparently been down since fall 2014. The fact that it has not been put back up may be evidence that the database behind the wiki was fatally corrupted (which I have seen happen to other wikis that use the traditional wiki software on personally-owned serves; note that wikidot, which hosts PhyloWiki and thousands of other wikis, should avoid this fate).
Some of the old help files were archived at archive.org:
http://web.archive.org/web/20140530041823/http://tnt.insectmuseum.org/index.php/Main_Page
http://web.archive.org/web/*/http://tnt.insectmuseum.org/index.php/Scripts/*
I have reconstructed what I can at: TNTR (R functions and TNT scripts for common tasks), TNTwiki, and tnt.htm