guoyi.run

TNT Script for Maximum Parsimony Analysis (Phylogeny)

Usage

Place this script and your matrix tnt file filename under the folder that you call tnt or exe file is placed
Enter tnt
Enter command guoyi filename;

Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.
Search trees via implicit enumeration (ntax<=25, but not for eiw) or TBR Mult (1000 times) with branch swapping (25<ntax<75, also for ntax<=25 with eiw) or Mult with branch swapping and Xmult (use random sectorial searches, produce 50 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).
Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).
Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).
Map apomorphic characters on the consensus tree.
Calculate TL, CI, and RI.

For Windows users

tnt run guoyi.run filename datatype weight 0/K cons resample prefix;

For Linux and Mac users

tnt run guoyi.run filename datatype weight 0/K cons resample prefix,

datatype should be 32, dna, prot, num or any types tnt allowed
- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
weight should be iw, ew, eiw
- iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw)
K is 12 (default) following Goloboff et al. 2017 (Cladistics 34: 407–437)
- it must more than 0
cons should be str, mjr, hlf
- mjr=majority rule, hlf=half, str=strict (default)
resample should be sum of what you want
- relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. rbrs+jak+boot+sym=7.1 (default)
prefix can be empty or a string
- default is empty

Results instructions are at the end of tnt.log.
*.tre are trees with taxname, *_no.tre are trees without taxname.
*.tnt.tre can be read by TNT/WinClada directly.
*.ctf can only be read by TNT via shortread.
*.svg is the tree file, which can be edited by inkscape
original* is the consensus tree.
apo.tre is the apomorphic character mapping tree.
resample.tre is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
trees*.tre contains he MPTs, which can be read by figtree after processing by tnt2figtree.
resample/apo.log contains the tree tags.
eiw.log contains character concavities.
homo.log contains homoplasy report of all characters.
report.log contains CI RI TL.
winclada.ss includes data matrix and consensus tree and it can be read by winclada directly.
winclada.tre can be transferred to the acceptable format for WinClada by tnt2winclada and the output file can be put into Winclada with your tnt matrix file filename for mapping apomorphic characters and homoplasy.

Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.

To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.

runwincladtree.run can handle wincladtree script with input file which must be $(PREFIX).winclada.ss or winclada.tree.