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

• Estimate implied weighting K value.

• Search trees via TBR Mult (1000 times) and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing).

• Perform 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

• 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.

• nelsen can be replaced by majority.

• xmult and mult replications and hold trees number can be adjusted.

• 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

g++ tnt2winclada.cpp -o tnt2winclada

or

clang++ -o tnt2winclada tnt2winclada.cpp

Windows

cl /EHsc tnt2winclada.cpp

Usage

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

Interactive commands are also available.