/usr/share/hyphy/SubstitutionClasses/nuc.bf is in hyphy-common 2.2.7+dfsg-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 | TemplateNames = {{
"Transitions",
"Transversions"
}};
SubClassNames = {{
"Purines",
"Pyrimidines"
}};
function CreateTemplates (classID)
{
if (classID==0)
{
MatrixTemplate = {{2,7,8,13}};
}
else
{
if (classID==1)
{
MatrixTemplate = {{1,3,4,6,9,11,12,14}};
}
}
return 0;
}
function CreateSubClasses (classID)
{
if (classID==0)
{
MatrixTemplate = {{0,2}};
}
else
{
if (classID==1)
{
MatrixTemplate = {{1,3}};
}
}
return 0;
}
|