TNT_Script/README.md

TNT Script used by Guoyi

The TNT script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).

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;

Functions

• Extended implied weighting with K value setting (default, default K=12) or implighted weighting with K value setting (default K=12) or equal weighting.

• Search trees via implicit enumeration (ntax<=25) or TBR Mult (1000 times) (25<ntax<75) or Mult and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).

• Perform Strict consensus / Majority-rule consensus / Half strict consensus.

• Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).

• Map apomorphic characters on the consensus tree.

• Calculate TL, CI, and RI.

Options

For Windows users

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

For Linux and Mac users

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

• datatpye should be 32, dna, prot, num

  • 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)

• cons should be str, mjr, hlf

  • mjr=majority rule, hlf=half, str=strict (default)

• resample should be sum of what you want

  • jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)

Results

• Results instructions are at the end of tnt.log.

• trees.tre, resample.tre are trees with taxname.

• trees_no.tre, resample_no.tre are trees without taxname.

• 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

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

TNT2WinClada

~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
 | | \| |   /_   \/\/ || ||_|(_|(_|(_|

MIT, Guoyi Zhang, 2023

Function

Convert TNT output tree file without tags and taxname, e.g. winclada.tre produced by TNT script, to WinClada acceptable format tree.

Compile

Linux & Unix

mkdir -p build && cd build
cmake ..
make && make install

Windows

cl /EHsc tnt2winclada.cpp

Usage

tnt2winclada -i ${input_file} -o ${output_file}

Interactive commands are also available.

tnt2winclada

~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
 | | \| |   /_   \/\/ || ||_|(_|(_|(_|
TNT2WinClada
MIT, Guoyi Zhang, 2023
please type help to see more commands

tnt2winclada> help
help			show interactive commands help
input <filename>	input a TNT output tree from the specified file
output <filename>	output a winclada accessible tree file
quit			quit the program
exit			exit the program

tnt2winclada>