Because I am fed up with figuring it out anew every time I need to use the Incongruence Length Difference (ILD) test (Farris et al., 1994) in TNT, I will post it once and for all here:
Download TNT and the script "ildtnt.run" from PhyloWiki. In the script, you may have to replace all instances of "numreps" with "num_reps" to make it functional. I at least get the error "numreps is a reserved expression", suggesting that the programmer should not have used that as a variable name.
Open TNT, increase memory, and set data to DNA and treating gaps as missing data. Then load your data matrix, which should of course be in TNT format:
mxram 200 ;
nstates DNA ;
nstates NOGAPS ;
proc (your_alignment_file_name) ;
Look up how many characters your first partition has, then run the test with:
run ildtnt.run (length_of_first_partition) (replicates) ;
There is an alternative script for doing the test called Ild.run, but I have so far failed to set the number of user variables high enough to accommodate my datasets. They seem to be limited to 1,000?
Perhaps this guide will also be useful to somebody besides me.
Farris JS, Källersjö M, Kluge AG, Bult C, 1994. Testing significance of incongruence. Cladistics 10: 315-319.