CMakeLists.txt | ||
guoyi.run | ||
LICENSE | ||
README.md | ||
tnt2winclada.cpp |
TNT Script used by Guoyi
The TNT script follows MIT license.
Usage
-
Place this script and your matrix tnt file
filename
under the folder that you calltnt
orexe
file is placed -
Enter
tnt
-
Enter command
guoyi filename;
Functions
-
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 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 jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
-
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 prefix;
For Linux and Mac users
tnt run guoyi.run filename datatype weight K cons resample prefix,
-
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)
-
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
- jak=1, boot=2, bremer=4 sym=8 i.e. jak+boot+sym+bremer=15 (default)
-
prefix can be empty or a string
- default is empty
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 filefilename
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>