TNT_Script/README.md

TNT Script used by Guoyi

This 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

• Estimated implied weighting K value.

• Search trees via TBR Mult and Xmult.

• Perform Strict consensus.

• Calculate Relative Bremer support, jackknifing, and bootstrap.

• Calculate TL, CI, and RI.

Options

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

• trees.tre, con.tre are trees with taxaname.

• trees_no.tre, con_no.tre are trees without taxaname.

• con_no.tre can be put into Winclada with your tnt matrix file filename.

• nelsen can be replaced by majority.

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