/usr/lib/R/site-library/phylobase/nexusfiles/minNex.nex is in r-cran-phylobase 0.8.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 | #NEXUS
BEGIN TAXA;
DIMENSIONS NTAX=4;
TAXLABELS
spA spB spC spD
;
END;
BEGIN TREES;
TRANSLATE
1 spA,
2 spB,
3 spC,
4 spD;
TREE testTree = (1,(2,(3,4)));
END;
BEGIN CHARACTERS;
TITLE 'TestContinuous';
DIMENSIONS NCHAR=3;
FORMAT DATATYPE = CONTINUOUS;
CHARSTATELABELS
1 char1,
2 char2,
3 char3;
MATRIX
spB 0.21 0.22 0.23
spA 0.11 0.12 0.13
spD 0.41 0.42 0.43
spC 0.31 0.32 0.33
;
END;
BEGIN CHARACTERS;
TITLE 'TestStd';
DIMENSIONS NCHAR=3;
FORMAT DATATYPE = STANDARD
MISSING = ?
SYMBOLS = "0 1 2";
CHARSTATELABELS
1 char1 / state11 state12 state13,
2 char2 / state21 state22 state23,
3 char3 / state31 state32 state33;
MATRIX
spA 1 (0 1) ?
spB 2 (1 2) 0
spC 0 (0 1 2) 1
spD 1 2 0
;
END;
[BEGIN ASSUMPTIONS;
EXSET * UNTITLED = 3;
END;]
|