/usr/share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf 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.
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alignOptions ["SEQ_ALIGN_CHARACTER_MAP"]="ARNDCQEGHILKMFPSTWYV";
ChoiceList (refSeq,"Scoring Matrix",1,SKIP_NONE,"BLOSUM62","Default BLAST BLOSUM62 matrix",
"HIV 5%","Empirically derived 5% divergence HIV matrix",
"HIV 25%","Empirically derived 25% divergence HIV matrix",
"HIV 50%","Empirically derived 50% divergence HIV matrix");
if (refSeq < 0)
{
return 0;
}
if (refSeq == 0)
{
/*
# Divergence level: 0.38
# Matrix from: TeraMonkey:Users:sergei:hyphy:trunk:TemplateBatchFiles:TemplateModels:EmpiricalAA:BLOSUM62
# Expected score: -0.548341 Entropy: 4.88752 bits
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 6 -3 -4 -4 -2 -2 -2 -1 -3 -3 -3 -2 -2 -4 -2 0 -1 -5 -3 -1 -4 -2 -2 -7
R -3 8 -2 -4 -6 0 -2 -5 -2 -6 -4 1 -3 -5 -4 -2 -3 -5 -3 -5 -3 -1 -2 -7
N -4 -2 8 0 -5 -1 -2 -2 0 -6 -6 -1 -4 -5 -4 0 -1 -7 -4 -5 6 -2 -2 -7
D -4 -4 0 8 -6 -2 0 -3 -3 -5 -6 -2 -6 -6 -3 -1 -3 -7 -6 -6 6 0 -3 -7
C -2 -6 -5 -6 10 -5 -7 -5 -5 -3 -3 -6 -3 -5 -5 -2 -2 -4 -4 -2 -5 -6 -4 -7
Q -2 0 -1 -2 -5 8 1 -4 0 -6 -4 0 -1 -6 -3 -1 -2 -3 -3 -4 -1 6 -2 -7
E -2 -2 -2 0 -7 1 7 -4 -1 -6 -5 0 -4 -6 -3 -1 -2 -5 -4 -4 0 6 -2 -7
G -1 -5 -2 -3 -5 -4 -4 7 -4 -7 -6 -3 -5 -5 -4 -2 -4 -4 -5 -6 -2 -4 -4 -7
H -3 -2 0 -3 -5 0 -1 -4 10 -6 -5 -2 -3 -3 -4 -2 -4 -5 0 -6 -1 -1 -3 -7
I -3 -6 -6 -5 -3 -6 -6 -7 -6 6 0 -5 0 -1 -5 -5 -2 -5 -3 2 -5 -6 -2 -7
L -3 -4 -6 -6 -3 -4 -5 -6 -5 0 6 -5 1 -1 -5 -5 -3 -3 -3 0 -6 -5 -2 -7
K -2 1 -1 -2 -6 0 0 -3 -2 -5 -5 7 -3 -6 -2 -1 -2 -5 -3 -4 -2 0 -2 -7
M -2 -3 -4 -6 -3 -1 -4 -5 -3 0 1 -3 9 -1 -5 -3 -2 -3 -3 0 -5 -2 -1 -7
F -4 -5 -5 -6 -5 -6 -6 -5 -3 -1 -1 -6 -1 8 -6 -4 -4 0 1 -3 -6 -6 -3 -7
P -2 -4 -4 -3 -5 -3 -3 -4 -4 -5 -5 -2 -5 -6 9 -2 -3 -6 -5 -4 -4 -3 -4 -7
S 0 -2 0 -1 -2 -1 -1 -2 -2 -5 -5 -1 -3 -4 -2 7 0 -5 -3 -4 -1 -1 -2 -7
T -1 -3 -1 -3 -2 -2 -2 -4 -4 -2 -3 -2 -2 -4 -3 0 7 -4 -3 -1 -2 -2 -2 -7
W -5 -5 -7 -7 -4 -3 -5 -4 -5 -5 -3 -5 -3 0 -6 -5 -4 12 0 -6 -7 -4 -4 -7
Y -3 -3 -4 -6 -4 -3 -4 -5 0 -3 -3 -3 -3 1 -5 -3 -3 0 9 -3 -5 -3 -2 -7
V -1 -5 -5 -6 -2 -4 -4 -6 -6 2 0 -4 0 -3 -4 -4 -1 -6 -3 6 -6 -4 -2 -7
B -4 -3 6 6 -5 -1 0 -2 -1 -5 -6 -2 -5 -6 -4 -1 -2 -7 -5 -6 7 -1 -3 -7
Z -2 -1 -2 0 -6 6 6 -4 -1 -6 -5 0 -2 -6 -3 -1 -2 -4 -3 -4 -1 7 -2 -7
X -2 -2 -2 -3 -4 -2 -2 -4 -3 -2 -2 -2 -1 -3 -4 -2 -2 -4 -2 -2 -3 -2 -2 -7
* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
*/
scoreMatrix =
{
{ 6, -3, -4, -4, -2, -2, -2, -1, -3, -3, -3, -2, -2, -4, -2, 0, -1, -5, -3, -1, -4, -2, -2, -7}
{ -3, 8, -2, -4, -6, 0, -2, -5, -2, -6, -4, 1, -3, -5, -4, -2, -3, -5, -3, -5, -3, -1, -2, -7}
{ -4, -2, 8, 0, -5, -1, -2, -2, 0, -6, -6, -1, -4, -5, -4, 0, -1, -7, -4, -5, 6, -2, -2, -7}
{ -4, -4, 0, 8, -6, -2, 0, -3, -3, -5, -6, -2, -6, -6, -3, -1, -3, -7, -6, -6, 6, 0, -3, -7}
{ -2, -6, -5, -6, 10, -5, -7, -5, -5, -3, -3, -6, -3, -5, -5, -2, -2, -4, -4, -2, -5, -6, -4, -7}
{ -2, 0, -1, -2, -5, 8, 1, -4, 0, -6, -4, 0, -1, -6, -3, -1, -2, -3, -3, -4, -1, 6, -2, -7}
{ -2, -2, -2, 0, -7, 1, 7, -4, -1, -6, -5, 0, -4, -6, -3, -1, -2, -5, -4, -4, 0, 6, -2, -7}
{ -1, -5, -2, -3, -5, -4, -4, 7, -4, -7, -6, -3, -5, -5, -4, -2, -4, -4, -5, -6, -2, -4, -4, -7}
{ -3, -2, 0, -3, -5, 0, -1, -4, 10, -6, -5, -2, -3, -3, -4, -2, -4, -5, 0, -6, -1, -1, -3, -7}
{ -3, -6, -6, -5, -3, -6, -6, -7, -6, 6, 0, -5, 0, -1, -5, -5, -2, -5, -3, 2, -5, -6, -2, -7}
{ -3, -4, -6, -6, -3, -4, -5, -6, -5, 0, 6, -5, 1, -1, -5, -5, -3, -3, -3, 0, -6, -5, -2, -7}
{ -2, 1, -1, -2, -6, 0, 0, -3, -2, -5, -5, 7, -3, -6, -2, -1, -2, -5, -3, -4, -2, 0, -2, -7}
{ -2, -3, -4, -6, -3, -1, -4, -5, -3, 0, 1, -3, 9, -1, -5, -3, -2, -3, -3, 0, -5, -2, -1, -7}
{ -4, -5, -5, -6, -5, -6, -6, -5, -3, -1, -1, -6, -1, 8, -6, -4, -4, 0, 1, -3, -6, -6, -3, -7}
{ -2, -4, -4, -3, -5, -3, -3, -4, -4, -5, -5, -2, -5, -6, 9, -2, -3, -6, -5, -4, -4, -3, -4, -7}
{ 0, -2, 0, -1, -2, -1, -1, -2, -2, -5, -5, -1, -3, -4, -2, 7, 0, -5, -3, -4, -1, -1, -2, -7}
{ -1, -3, -1, -3, -2, -2, -2, -4, -4, -2, -3, -2, -2, -4, -3, 0, 7, -4, -3, -1, -2, -2, -2, -7}
{ -5, -5, -7, -7, -4, -3, -5, -4, -5, -5, -3, -5, -3, 0, -6, -5, -4, 12, 0, -6, -7, -4, -4, -7}
{ -3, -3, -4, -6, -4, -3, -4, -5, 0, -3, -3, -3, -3, 1, -5, -3, -3, 0, 9, -3, -5, -3, -2, -7}
{ -1, -5, -5, -6, -2, -4, -4, -6, -6, 2, 0, -4, 0, -3, -4, -4, -1, -6, -3, 6, -6, -4, -2, -7}
{ -4, -3, 6, 6, -5, -1, 0, -2, -1, -5, -6, -2, -5, -6, -4, -1, -2, -7, -5, -6, 7, -1, -3, -7}
{ -2, -1, -2, 0, -6, 6, 6, -4, -1, -6, -5, 0, -2, -6, -3, -1, -2, -4, -3, -4, -1, 7, -2, -7}
{ -2, -2, -2, -3, -4, -2, -2, -4, -3, -2, -2, -2, -1, -3, -4, -2, -2, -4, -2, -2, -3, -2, -2, -7}
{ -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, 1}
};
}
if (refSeq == 1)
{
// HIV-1 between 5%
/*
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 8 -13 -16 -8 -15 -17 -8 -7 -16 -14 -14 -17 -16 -20 -7 -7 -2 -23 -23 -4 -10 -10 -8 -24
R -13 8 -12 -20 -12 -6 -15 -6 -3 -11 -11 -1 -7 -21 -9 -6 -7 -10 -18 -16 -14 -8 -7 -24
N -16 -12 9 -1 -15 -11 -14 -12 -4 -11 -20 -4 -19 -20 -17 -2 -4 -24 -8 -18 7 -12 -7 -24
D -8 -20 -1 9 -22 -19 -3 -7 -8 -19 -22 -15 -22 -23 -19 -11 -13 -23 -11 -9 7 -4 -7 -24
C -15 -12 -15 -22 11 -23 -23 -10 -13 -19 -15 -21 -22 -3 -20 -5 -10 -7 -4 -12 -17 -23 -9 -24
Q -17 -6 -11 -19 -23 8 -7 -17 -4 -20 -8 -4 -13 -20 -5 -15 -13 -20 -15 -20 -12 6 -8 -24
E -8 -15 -14 -3 -23 -7 8 -6 -15 -20 -23 -5 -14 -24 -20 -19 -13 -23 -17 -9 -5 6 -9 -24
G -7 -6 -12 -7 -10 -17 -6 7 -19 -20 -22 -11 -21 -13 -20 -5 -12 -9 -22 -10 -8 -7 -9 -24
H -16 -3 -4 -8 -13 -4 -15 -19 11 -16 -8 -14 -19 -13 -7 -12 -10 -17 -1 -22 -5 -6 -7 -24
I -14 -11 -11 -19 -19 -20 -20 -20 -16 7 -4 -13 -3 -6 -17 -9 -3 -22 -15 -1 -12 -20 -7 -24
L -14 -11 -20 -22 -15 -8 -23 -22 -8 -4 7 -16 -5 -3 -7 -10 -16 -10 -15 -8 -21 -11 -9 -24
K -17 -1 -4 -15 -21 -4 -5 -11 -14 -13 -16 8 -9 -19 -17 -11 -5 -20 -22 -13 -6 -5 -6 -24
M -16 -7 -19 -22 -22 -13 -14 -21 -19 -3 -5 -9 11 -13 -20 -18 -5 -16 -23 -4 -20 -14 -7 -24
F -20 -21 -20 -23 -3 -20 -24 -13 -13 -6 -3 -19 -13 10 -19 -10 -18 -10 -2 -10 -21 -22 -8 -24
P -7 -9 -17 -19 -20 -5 -20 -20 -7 -17 -7 -17 -20 -19 9 -5 -8 -18 -18 -20 -18 -8 -9 -24
S -7 -6 -2 -11 -5 -15 -19 -5 -12 -9 -10 -11 -18 -10 -5 8 -3 -19 -11 -16 -4 -17 -7 -24
T -2 -7 -4 -13 -10 -13 -13 -12 -10 -3 -16 -5 -5 -18 -8 -3 8 -23 -16 -10 -6 -13 -6 -24
W -23 -10 -24 -23 -7 -20 -23 -9 -17 -22 -10 -20 -16 -10 -18 -19 -23 10 -9 -23 -23 -21 -12 -24
Y -23 -18 -8 -11 -4 -15 -17 -22 -1 -15 -15 -22 -23 -2 -18 -11 -16 -9 10 -18 -9 -16 -9 -24
V -4 -16 -18 -9 -12 -20 -9 -10 -22 -1 -8 -13 -4 -10 -20 -16 -10 -23 -18 8 -11 -11 -7 -24
B -10 -14 7 7 -17 -12 -5 -8 -5 -12 -21 -6 -20 -21 -18 -4 -6 -23 -9 -11 8 -6 -8 -24
Z -10 -8 -12 -4 -23 6 6 -7 -6 -20 -11 -5 -14 -22 -8 -17 -13 -21 -16 -11 -6 7 -9 -24
X -8 -7 -7 -7 -9 -8 -9 -9 -7 -7 -9 -6 -7 -8 -9 -7 -6 -12 -9 -7 -8 -9 -8 -24
* -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 -24 1
*/
scoreMatrix =
{
{ 8, -13, -16, -8, -15, -17, -8, -7, -16, -14, -14, -17, -16, -20, -7, -7, -2, -23, -23, -4, -10, -10, -8, -24}
{ -13, 8, -12, -20, -12, -6, -15, -6, -3, -11, -11, -1, -7, -21, -9, -6, -7, -10, -18, -16, -14, -8, -7, -24}
{ -16, -12, 9, -1, -15, -11, -14, -12, -4, -11, -20, -4, -19, -20, -17, -2, -4, -24, -8, -18, 7, -12, -7, -24}
{ -8, -20, -1, 9, -22, -19, -3, -7, -8, -19, -22, -15, -22, -23, -19, -11, -13, -23, -11, -9, 7, -4, -7, -24}
{ -15, -12, -15, -22, 11, -23, -23, -10, -13, -19, -15, -21, -22, -3, -20, -5, -10, -7, -4, -12, -17, -23, -9, -24}
{ -17, -6, -11, -19, -23, 8, -7, -17, -4, -20, -8, -4, -13, -20, -5, -15, -13, -20, -15, -20, -12, 6, -8, -24}
{ -8, -15, -14, -3, -23, -7, 8, -6, -15, -20, -23, -5, -14, -24, -20, -19, -13, -23, -17, -9, -5, 6, -9, -24}
{ -7, -6, -12, -7, -10, -17, -6, 7, -19, -20, -22, -11, -21, -13, -20, -5, -12, -9, -22, -10, -8, -7, -9, -24}
{ -16, -3, -4, -8, -13, -4, -15, -19, 11, -16, -8, -14, -19, -13, -7, -12, -10, -17, -1, -22, -5, -6, -7, -24}
{ -14, -11, -11, -19, -19, -20, -20, -20, -16, 7, -4, -13, -3, -6, -17, -9, -3, -22, -15, -1, -12, -20, -7, -24}
{ -14, -11, -20, -22, -15, -8, -23, -22, -8, -4, 7, -16, -5, -3, -7, -10, -16, -10, -15, -8, -21, -11, -9, -24}
{ -17, -1, -4, -15, -21, -4, -5, -11, -14, -13, -16, 8, -9, -19, -17, -11, -5, -20, -22, -13, -6, -5, -6, -24}
{ -16, -7, -19, -22, -22, -13, -14, -21, -19, -3, -5, -9, 11, -13, -20, -18, -5, -16, -23, -4, -20, -14, -7, -24}
{ -20, -21, -20, -23, -3, -20, -24, -13, -13, -6, -3, -19, -13, 10, -19, -10, -18, -10, -2, -10, -21, -22, -8, -24}
{ -7, -9, -17, -19, -20, -5, -20, -20, -7, -17, -7, -17, -20, -19, 9, -5, -8, -18, -18, -20, -18, -8, -9, -24}
{ -7, -6, -2, -11, -5, -15, -19, -5, -12, -9, -10, -11, -18, -10, -5, 8, -3, -19, -11, -16, -4, -17, -7, -24}
{ -2, -7, -4, -13, -10, -13, -13, -12, -10, -3, -16, -5, -5, -18, -8, -3, 8, -23, -16, -10, -6, -13, -6, -24}
{ -23, -10, -24, -23, -7, -20, -23, -9, -17, -22, -10, -20, -16, -10, -18, -19, -23, 10, -9, -23, -23, -21, -12, -24}
{ -23, -18, -8, -11, -4, -15, -17, -22, -1, -15, -15, -22, -23, -2, -18, -11, -16, -9, 10, -18, -9, -16, -9, -24}
{ -4, -16, -18, -9, -12, -20, -9, -10, -22, -1, -8, -13, -4, -10, -20, -16, -10, -23, -18, 8, -11, -11, -7, -24}
{ -10, -14, 7, 7, -17, -12, -5, -8, -5, -12, -21, -6, -20, -21, -18, -4, -6, -23, -9, -11, 8, -6, -8, -24}
{ -10, -8, -12, -4, -23, 6, 6, -7, -6, -20, -11, -5, -14, -22, -8, -17, -13, -21, -16, -11, -6, 7, -9, -24}
{ -8, -7, -7, -7, -9, -8, -9, -9, -7, -7, -9, -6, -7, -8, -9, -7, -6, -12, -9, -7, -8, -9, -8, -24}
{ -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, -24, 1}
};
}
if (refSeq == 2)
{
// HIV-1 between 25%
/*
# Divergence level: 0.25
# Matrix from: TeraMonkey:Users:sergei:hyphy:trunk:TemplateBatchFiles:TemplateModels:EmpiricalAA:HIVBetween
# Expected score: -1.40621 Entropy: 5.90658 bits
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 7 -7 -7 -4 -10 -11 -4 -3 -10 -6 -9 -9 -7 -13 -3 -2 1 -16 -15 0 -5 -5 -3 -17
R -7 7 -5 -11 -8 -2 -7 -2 0 -6 -6 2 -3 -12 -4 -2 -2 -5 -9 -10 -7 -3 -3 -17
N -7 -5 8 2 -9 -6 -6 -7 0 -6 -12 0 -10 -12 -9 1 0 -17 -3 -10 6 -6 -3 -17
D -4 -11 2 8 -14 -10 0 -2 -3 -11 -15 -7 -13 -15 -13 -5 -6 -16 -6 -5 7 0 -3 -17
C -10 -8 -9 -14 11 -16 -15 -5 -7 -11 -9 -13 -14 0 -12 -1 -6 -2 0 -8 -10 -16 -5 -17
Q -11 -2 -6 -10 -16 8 -2 -10 0 -12 -4 0 -8 -12 -1 -9 -8 -14 -9 -13 -7 6 -4 -17
E -4 -7 -6 0 -15 -2 7 -1 -9 -12 -15 -1 -10 -17 -13 -11 -8 -15 -12 -5 0 6 -4 -17
G -3 -2 -7 -2 -5 -10 -1 7 -10 -11 -14 -6 -12 -9 -11 -1 -7 -5 -14 -5 -4 -3 -4 -17
H -10 0 0 -3 -7 0 -9 -10 10 -10 -4 -5 -10 -6 -3 -6 -6 -11 2 -14 -1 -2 -3 -17
I -6 -6 -6 -11 -11 -12 -12 -11 -10 7 0 -7 0 -2 -10 -4 0 -14 -9 2 -7 -12 -2 -17
L -9 -6 -12 -15 -9 -4 -15 -14 -4 0 6 -10 0 0 -3 -5 -8 -6 -8 -4 -13 -6 -4 -17
K -9 2 0 -7 -13 0 -1 -6 -5 -7 -10 7 -4 -14 -9 -5 -1 -12 -13 -9 -1 -1 -2 -17
M -7 -3 -10 -13 -14 -8 -10 -12 -10 0 0 -4 10 -7 -11 -9 -1 -11 -15 0 -11 -9 -3 -17
F -13 -12 -12 -15 0 -12 -17 -9 -6 -2 0 -14 -7 10 -11 -5 -10 -5 1 -5 -13 -14 -3 -17
P -3 -4 -9 -13 -12 -1 -13 -11 -3 -10 -3 -9 -11 -11 8 -1 -3 -13 -11 -12 -10 -3 -5 -17
S -2 -2 1 -5 -1 -9 -11 -1 -6 -4 -5 -5 -9 -5 -1 8 0 -12 -6 -9 0 -10 -3 -17
T 1 -2 0 -6 -6 -8 -8 -7 -6 0 -8 -1 -1 -10 -3 0 7 -16 -10 -4 -2 -8 -2 -17
W -16 -5 -17 -16 -2 -14 -15 -5 -11 -14 -6 -12 -11 -5 -13 -12 -16 10 -4 -16 -16 -14 -8 -17
Y -15 -9 -3 -6 0 -9 -12 -14 2 -9 -8 -13 -15 1 -11 -6 -10 -4 10 -12 -4 -10 -4 -17
V 0 -10 -10 -5 -8 -13 -5 -5 -14 2 -4 -9 0 -5 -12 -9 -4 -16 -12 7 -7 -7 -3 -17
B -5 -7 6 7 -10 -7 0 -4 -1 -7 -13 -1 -11 -13 -10 0 -2 -16 -4 -7 7 -2 -4 -17
Z -5 -3 -6 0 -16 6 6 -3 -2 -12 -6 -1 -9 -14 -3 -10 -8 -14 -10 -7 -2 6 -4 -17
X -3 -3 -3 -3 -5 -4 -4 -4 -3 -2 -4 -2 -3 -3 -5 -3 -2 -8 -4 -3 -4 -4 -3 -17
* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
*/
scoreMatrix =
{
{ 7, -7, -7, -4, -10, -11, -4, -3, -10, -6, -9, -9, -7, -13, -3, -2, 1, -16, -15, 0, -5, -5, -3, -17}
{ -7, 7, -5, -11, -8, -2, -7, -2, 0, -6, -6, 2, -3, -12, -4, -2, -2, -5, -9, -10, -7, -3, -3, -17}
{ -7, -5, 8, 2, -9, -6, -6, -7, 0, -6, -12, 0, -10, -12, -9, 1, 0, -17, -3, -10, 6, -6, -3, -17}
{ -4, -11, 2, 8, -14, -10, 0, -2, -3, -11, -15, -7, -13, -15, -13, -5, -6, -16, -6, -5, 7, 0, -3, -17}
{ -10, -8, -9, -14, 11, -16, -15, -5, -7, -11, -9, -13, -14, 0, -12, -1, -6, -2, 0, -8, -10, -16, -5, -17}
{ -11, -2, -6, -10, -16, 8, -2, -10, 0, -12, -4, 0, -8, -12, -1, -9, -8, -14, -9, -13, -7, 6, -4, -17}
{ -4, -7, -6, 0, -15, -2, 7, -1, -9, -12, -15, -1, -10, -17, -13, -11, -8, -15, -12, -5, 0, 6, -4, -17}
{ -3, -2, -7, -2, -5, -10, -1, 7, -10, -11, -14, -6, -12, -9, -11, -1, -7, -5, -14, -5, -4, -3, -4, -17}
{ -10, 0, 0, -3, -7, 0, -9, -10, 10, -10, -4, -5, -10, -6, -3, -6, -6, -11, 2, -14, -1, -2, -3, -17}
{ -6, -6, -6, -11, -11, -12, -12, -11, -10, 7, 0, -7, 0, -2, -10, -4, 0, -14, -9, 2, -7, -12, -2, -17}
{ -9, -6, -12, -15, -9, -4, -15, -14, -4, 0, 6, -10, 0, 0, -3, -5, -8, -6, -8, -4, -13, -6, -4, -17}
{ -9, 2, 0, -7, -13, 0, -1, -6, -5, -7, -10, 7, -4, -14, -9, -5, -1, -12, -13, -9, -1, -1, -2, -17}
{ -7, -3, -10, -13, -14, -8, -10, -12, -10, 0, 0, -4, 10, -7, -11, -9, -1, -11, -15, 0, -11, -9, -3, -17}
{ -13, -12, -12, -15, 0, -12, -17, -9, -6, -2, 0, -14, -7, 10, -11, -5, -10, -5, 1, -5, -13, -14, -3, -17}
{ -3, -4, -9, -13, -12, -1, -13, -11, -3, -10, -3, -9, -11, -11, 8, -1, -3, -13, -11, -12, -10, -3, -5, -17}
{ -2, -2, 1, -5, -1, -9, -11, -1, -6, -4, -5, -5, -9, -5, -1, 8, 0, -12, -6, -9, 0, -10, -3, -17}
{ 1, -2, 0, -6, -6, -8, -8, -7, -6, 0, -8, -1, -1, -10, -3, 0, 7, -16, -10, -4, -2, -8, -2, -17}
{ -16, -5, -17, -16, -2, -14, -15, -5, -11, -14, -6, -12, -11, -5, -13, -12, -16, 10, -4, -16, -16, -14, -8, -17}
{ -15, -9, -3, -6, 0, -9, -12, -14, 2, -9, -8, -13, -15, 1, -11, -6, -10, -4, 10, -12, -4, -10, -4, -17}
{ 0, -10, -10, -5, -8, -13, -5, -5, -14, 2, -4, -9, 0, -5, -12, -9, -4, -16, -12, 7, -7, -7, -3, -17}
{ -5, -7, 6, 7, -10, -7, 0, -4, -1, -7, -13, -1, -11, -13, -10, 0, -2, -16, -4, -7, 7, -2, -4, -17}
{ -5, -3, -6, 0, -16, 6, 6, -3, -2, -12, -6, -1, -9, -14, -3, -10, -8, -14, -10, -7, -2, 6, -4, -17}
{ -3, -3, -3, -3, -5, -4, -4, -4, -3, -2, -4, -2, -3, -3, -5, -3, -2, -8, -4, -3, -4, -4, -3, -17}
{ -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, -17, 1}
};
}
if (refSeq == 3)
{
/*
# Divergence level: 0.5
# Matrix from: TeraMonkey:Users:sergei:hyphy:trunk:TemplateBatchFiles:TemplateModels:EmpiricalAA:HIVBetween
# Expected score: -0.849814 Entropy: 4.53171 bits
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 7 -5 -4 -2 -7 -8 -2 -1 -8 -2 -6 -5 -4 -9 -1 -1 2 -13 -12 1 -3 -4 -2 -13
R -5 6 -2 -7 -6 0 -4 0 1 -4 -4 3 -1 -9 -3 0 -1 -4 -6 -7 -4 -1 -1 -13
N -4 -2 7 3 -6 -3 -3 -4 0 -4 -8 0 -7 -8 -5 2 0 -13 -2 -7 6 -3 -1 -13
D -2 -7 3 8 -10 -6 2 -1 -1 -8 -12 -4 -10 -11 -9 -2 -4 -12 -4 -4 6 0 -2 -13
C -7 -6 -6 -10 11 -12 -12 -3 -4 -7 -6 -9 -10 2 -8 0 -4 0 1 -6 -7 -12 -3 -13
Q -8 0 -3 -6 -12 7 -1 -7 1 -8 -2 0 -6 -8 0 -6 -5 -11 -6 -10 -5 5 -2 -13
E -2 -4 -3 2 -12 -1 7 0 -6 -8 -11 0 -7 -13 -9 -7 -5 -12 -9 -3 0 5 -2 -13
G -1 0 -4 -1 -3 -7 0 7 -7 -8 -10 -3 -9 -7 -8 0 -4 -3 -10 -4 -2 -1 -3 -13
H -8 1 0 -1 -4 1 -6 -7 9 -7 -2 -2 -7 -3 -1 -3 -4 -8 3 -10 0 -1 -1 -13
I -2 -4 -4 -8 -7 -8 -8 -8 -7 6 0 -5 2 0 -7 -3 0 -11 -7 3 -5 -8 -1 -13
L -6 -4 -8 -12 -6 -2 -11 -10 -2 0 6 -7 0 1 -1 -4 -5 -4 -5 -1 -10 -5 -3 -13
K -5 3 0 -4 -9 0 0 -3 -2 -5 -7 6 -3 -11 -6 -2 0 -9 -9 -6 0 0 -1 -13
M -4 -1 -7 -10 -10 -6 -7 -9 -7 2 0 -3 10 -4 -7 -6 0 -9 -10 1 -8 -6 -1 -13
F -9 -9 -8 -11 2 -8 -13 -7 -3 0 1 -11 -4 9 -7 -4 -7 -3 3 -3 -9 -10 -2 -13
P -1 -3 -5 -9 -8 0 -9 -8 -1 -7 -1 -6 -7 -7 8 0 -1 -11 -8 -8 -7 -2 -3 -13
S -1 0 2 -2 0 -6 -7 0 -3 -3 -4 -2 -6 -4 0 7 1 -9 -4 -6 0 -6 -1 -13
T 2 -1 0 -4 -4 -5 -5 -4 -4 0 -5 0 0 -7 -1 1 6 -12 -7 -1 0 -5 -1 -13
W -13 -4 -13 -12 0 -11 -12 -3 -8 -11 -4 -9 -9 -3 -11 -9 -12 10 -2 -12 -12 -11 -6 -13
Y -12 -6 -2 -4 1 -6 -9 -10 3 -7 -5 -9 -10 3 -8 -4 -7 -2 9 -9 -3 -7 -3 -13
V 1 -7 -7 -4 -6 -10 -3 -4 -10 3 -1 -6 1 -3 -8 -6 -1 -12 -9 6 -5 -5 -1 -13
B -3 -4 6 6 -7 -5 0 -2 0 -5 -10 0 -8 -9 -7 0 0 -12 -3 -5 7 0 -2 -13
Z -4 -1 -3 0 -12 5 5 -1 -1 -8 -5 0 -6 -10 -2 -6 -5 -11 -7 -5 0 6 -3 -13
X -2 -1 -1 -2 -3 -2 -2 -3 -1 -1 -3 -1 -1 -2 -3 -1 -1 -6 -3 -1 -2 -3 -2 -13
* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1
*/
scoreMatrix =
{
{ 7, -5, -4, -2, -7, -8, -2, -1, -8, -2, -6, -5, -4, -9, -1, -1, 2, -13, -12, 1, -3, -4, -2, -13}
{ -5, 6, -2, -7, -6, 0, -4, 0, 1, -4, -4, 3, -1, -9, -3, 0, -1, -4, -6, -7, -4, -1, -1, -13}
{ -4, -2, 7, 3, -6, -3, -3, -4, 0, -4, -8, 0, -7, -8, -5, 2, 0, -13, -2, -7, 6, -3, -1, -13}
{ -2, -7, 3, 8, -10, -6, 2, -1, -1, -8, -12, -4, -10, -11, -9, -2, -4, -12, -4, -4, 6, 0, -2, -13}
{ -7, -6, -6, -10, 11, -12, -12, -3, -4, -7, -6, -9, -10, 2, -8, 0, -4, 0, 1, -6, -7, -12, -3, -13}
{ -8, 0, -3, -6, -12, 7, -1, -7, 1, -8, -2, 0, -6, -8, 0, -6, -5, -11, -6, -10, -5, 5, -2, -13}
{ -2, -4, -3, 2, -12, -1, 7, 0, -6, -8, -11, 0, -7, -13, -9, -7, -5, -12, -9, -3, 0, 5, -2, -13}
{ -1, 0, -4, -1, -3, -7, 0, 7, -7, -8, -10, -3, -9, -7, -8, 0, -4, -3, -10, -4, -2, -1, -3, -13}
{ -8, 1, 0, -1, -4, 1, -6, -7, 9, -7, -2, -2, -7, -3, -1, -3, -4, -8, 3, -10, 0, -1, -1, -13}
{ -2, -4, -4, -8, -7, -8, -8, -8, -7, 6, 0, -5, 2, 0, -7, -3, 0, -11, -7, 3, -5, -8, -1, -13}
{ -6, -4, -8, -12, -6, -2, -11, -10, -2, 0, 6, -7, 0, 1, -1, -4, -5, -4, -5, -1, -10, -5, -3, -13}
{ -5, 3, 0, -4, -9, 0, 0, -3, -2, -5, -7, 6, -3, -11, -6, -2, 0, -9, -9, -6, 0, 0, -1, -13}
{ -4, -1, -7, -10, -10, -6, -7, -9, -7, 2, 0, -3, 10, -4, -7, -6, 0, -9, -10, 1, -8, -6, -1, -13}
{ -9, -9, -8, -11, 2, -8, -13, -7, -3, 0, 1, -11, -4, 9, -7, -4, -7, -3, 3, -3, -9, -10, -2, -13}
{ -1, -3, -5, -9, -8, 0, -9, -8, -1, -7, -1, -6, -7, -7, 8, 0, -1, -11, -8, -8, -7, -2, -3, -13}
{ -1, 0, 2, -2, 0, -6, -7, 0, -3, -3, -4, -2, -6, -4, 0, 7, 1, -9, -4, -6, 0, -6, -1, -13}
{ 2, -1, 0, -4, -4, -5, -5, -4, -4, 0, -5, 0, 0, -7, -1, 1, 6, -12, -7, -1, 0, -5, -1, -13}
{ -13, -4, -13, -12, 0, -11, -12, -3, -8, -11, -4, -9, -9, -3, -11, -9, -12, 10, -2, -12, -12, -11, -6, -13}
{ -12, -6, -2, -4, 1, -6, -9, -10, 3, -7, -5, -9, -10, 3, -8, -4, -7, -2, 9, -9, -3, -7, -3, -13}
{ 1, -7, -7, -4, -6, -10, -3, -4, -10, 3, -1, -6, 1, -3, -8, -6, -1, -12, -9, 6, -5, -5, -1, -13}
{ -3, -4, 6, 6, -7, -5, 0, -2, 0, -5, -10, 0, -8, -9, -7, 0, 0, -12, -3, -5, 7, 0, -2, -13}
{ -4, -1, -3, 0, -12, 5, 5, -1, -1, -8, -5, 0, -6, -10, -2, -6, -5, -11, -7, -5, 0, 6, -3, -13}
{ -2, -1, -1, -2, -3, -2, -2, -3, -1, -1, -3, -1, -1, -2, -3, -1, -1, -6, -3, -1, -2, -3, -2, -13}
{ -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, -13, 1}
};
}
alignOptions ["SEQ_ALIGN_SCORE_MATRIX"] = scoreMatrix[{{0,0}}][{{19,19}}];
alignOptions ["SEQ_ALIGN_GAP_OPEN"] = 40;
alignOptions ["SEQ_ALIGN_GAP_OPEN2"] = 20;
alignOptions ["SEQ_ALIGN_GAP_EXTEND"] = 10;
alignOptions ["SEQ_ALIGN_GAP_EXTEND2"] = 5;
alignOptions ["SEQ_ALIGN_AFFINE"] = 1;
ChoiceList (refSeq,"Prefix/Suffix Indels",1,SKIP_NONE,"No penalty","Do not penalize prefix and suffix Indels","Normal penalty","Treat prefix and suffix indels as any other indels");
if (refSeq < 0)
{
return 0;
}
alignOptions ["SEQ_ALIGN_NO_TP"] = 1-refSeq;
if (_skipPredefsSeqAlignShared == 0)
{
predefSeqNames = {{"First in file", "Use the first sequence in the data file as a reference"}
{"Longest in file", "Use the longest sequence in the data file as the reference"}
/*0*/ {"HXB2_env", "Use HIV-1 HXB2 reference strain envelope sequence (K03455)"}
/*1*/ {"HXB2_nef", "Use HIV-1 HXB2 reference strain NEF sequence (K03455)"}
/*2*/ {"HXB2_gag", "Use HIV-1 HXB2 reference strain gag sequence (K03455)"}
/*3*/ {"HXB2_vpr", "Use HIV-1 HXB2 reference strain vpr sequence (K03455)"}
/*4*/ {"HXB2_vif", "Use HIV-1 HXB2 reference strain vif sequence (K03455)"}
/*5*/ {"HXB2_vpu", "Use HIV-1 HXB2 reference strain vpu sequence (K03455)"}
/*6*/ {"HXB2_pr", "Use HIV-1 HXB2 reference strain protease sequence (K03455)"}
/*7*/ {"HXB2_rt", "Use HIV-1 HXB2 reference strain reverse transcriptase sequence (K03455)"}
/*8*/ {"HXB2_int", "Use HIV-1 HXB2 reference strain integrase sequence (K03455)"}
/*9*/ {"HXB2_rev", "Use HIV-1 HXB2 reference strain rev (exons 1 and 2)sequence (K03455)"}
/*10*/ {"HXB2_tat", "Use HIV-1 HXB2 reference strain tat (exons 1 and 2) sequence (K03455)"}
/*11*/ {"HXB2_prrt", "Use HIV-1 HXB2 reference strain protease+rt sequence (K03455)"}
/*12*/ {"NL4_3prrt", "Use HIV-1 NL4-3 reference strain pr+rt sequence"}
/*13*/ {"HXB2_pol", "Use HIV-1 HXB2 reference strain pol (starting at pr) sequence (K03455)"}
};
predefSeqNames2 = {{"No", "No reference coordinate sequences"}
/*0*/ {"HXB2_env", "Use HIV-1 HXB2 reference strain envelope sequence (K03455)"}
/*1*/ {"HXB2_nef", "Use HIV-1 HXB2 reference strain NEF sequence (K03455)"}
/*2*/ {"HXB2_gag", "Use HIV-1 HXB2 reference strain gag sequence (K03455)"}
/*3*/ {"HXB2_vpr", "Use HIV-1 HXB2 reference strain vpr sequence (K03455)"}
/*4*/ {"HXB2_vif", "Use HIV-1 HXB2 reference strain vif sequence (K03455)"}
/*5*/ {"HXB2_vpu", "Use HIV-1 HXB2 reference strain vpu sequence (K03455)"}
/*6*/ {"HXB2_pr", "Use HIV-1 HXB2 reference strain protease sequence (K03455)"}
/*7*/ {"HXB2_rt", "Use HIV-1 HXB2 reference strain reverse transcriptase sequence (K03455)"}
/*8*/ {"HXB2_int", "Use HIV-1 HXB2 reference strain integrase sequence (K03455)"}
/*9*/ {"HXB2_rev", "Use HIV-1 HXB2 reference strain rev (exons 1 and 2)sequence (K03455)"}
/*10*/ {"HXB2_tat", "Use HIV-1 HXB2 reference strain tat (exons 1 and 2) sequence (K03455)"}
/*11*/ {"HXB2_prrt", "Use HIV-1 HXB2 reference strain protease+rt sequence (K03455)"}
/*12*/ {"NL4_3prrt", "Use HIV-1 NL4-3 reference strain pr+rt sequence"}
/*13*/ {"HXB2_pol", "Use HIV-1 HXB2 reference strain pol (starting at pr) sequence (K03455)"}
};
RefSeqs = {};
RefSeqs [0] = "ATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTGGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTA";
RefSeqs [1] = "ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGAT---CAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC";
RefSeqs [2] = "ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAA";
RefSeqs [3] = "ATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACA---CAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAG---ATC";
RefSeqs [4] = "ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACAC";
RefSeqs [5] = "ACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATC";
RefSeqs [6] = "CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT";
RefSeqs [7] = "CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC";
RefSeqs [8] = "TTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGAT";
RefSeqs [9] = "ATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGA";
RefSeqs[10] = "ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGAT";
RefSeqs[11] = "CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC";
RefSeqs[12] = "CCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAGGACAGTATGATCAGATACTCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACAGTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAAGGGTGCCCACACTAATGATGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCATAATAGGAGCAGAAACTTTC";
RefSeqs[13] = "CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAG";
ChoiceList (refSeq,"Choose a reference sequence",1,SKIP_NONE,predefSeqNames);
if (refSeq < 0)
{
return 0;
}
}
//---------------------------------------------------------------------------------------------------------------------
function _handleAlignment (dataSetName, writeToFiles)
{
result = {};
ExecuteCommands ("DataSetFilter _alignmentHandlerFilter = CreateFilter ("+dataSetName+",1);");
GetInformation (UnalignedSeqs,_alignmentHandlerFilter );
//preprocess sequences
unalSequenceCount = Rows(UnalignedSeqs)*Columns(UnalignedSeqs);
GetString (sequenceNames, unal, -1);
longestSequence = 0;
longestSequenceIDX = 0;
for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
UnalignedSeqs[seqCounter] = ((UnalignedSeqs[seqCounter]^{{"[^a-zA-Z]",""}})^{{"^N+",""}})^{{"N+$",""}};
if (doLongestSequence)
{
if (doLongestSequence == 1 || seqCounter != unalSequenceCount-1)
{
if (Abs (UnalignedSeqs[seqCounter]) > longestSequence)
{
longestSequence = Abs (UnalignedSeqs[seqCounter]);
longestSequenceIDX = seqCounter;
}
}
}
}
if (doLongestSequence)
{
fprintf (stdout, "\nSelected sequence ", sequenceNames[longestSequenceIDX], " as reference.");
if (longestSequenceIDX > 0)
{
p1 = UnalignedSeqs[0];
UnalignedSeqs[0] = UnalignedSeqs[longestSequenceIDX];
UnalignedSeqs[longestSequenceIDX] = p1;
p1 = sequenceNames[0];
sequenceNames[0] = sequenceNames[longestSequenceIDX];
sequenceNames[longestSequenceIDX] = p1;
}
}
/* determine reading frames */
ProteinSequences = {};
AllTranslations = {};
ReadingFrames = {};
StopCodons = {};
StopPositions = {};
didRC = {};
fprintf (stdout, "\nDetecting reading frames for each sequence...\n");
frameCounter = {3,1};
stillHasStops = {};
for (seqCounter = 0; seqCounter < unalSequenceCount; seqCounter += 1)
{
aSeq = UnalignedSeqs[seqCounter];
seqLen = Abs(aSeq)-2;
minStops = 1e20;
tString = "";
rFrame = 0;
for (rc = 0; rc <= doRC; rc += 1)
{
stopPosn = {3,2};
allTran = {3,1};
if (rc)
{
aSeq = nucleotideReverseComplement (aSeq)
}
for (offset = 0; offset < 3; offset += 1)
{
translString = translateCodonToAA (aSeq, codonToAAMap, offset);
stopPos = translString||"X";
if (stopPos[0]>=0)
{
stopCount = Rows(stopPos)$2;
stopPosn[offset][0] = stopPos[0];
stopPosn[offset][1] = stopPos[stopCount*2-1];
}
else
{
stopCount = 0;
}
if (stopCount<minStops)
{
if (rc)
{
UnalignedSeqs[seqCounter] = aSeq;
didRC[seqCounter] = 1;
}
minStops = stopCount;
rFrame = offset;
tString = translString;
}
allTran[offset] = translString;
}
}
ReadingFrames[seqCounter] = rFrame;
ProteinSequences[seqCounter] = tString;
frameCounter[rFrame] = frameCounter[rFrame]+1;
StopPositions[seqCounter] = stopPosn;
AllTranslations [seqCounter] = allTran;
if (minStops>0)
{
stillHasStops[Abs(stillHasStops)] = seqCounter;
assert (seqCounter > 0, "Reference sequence must not contain frameshifts\n");
}
}
s1 = ProteinSequences[0];
fprintf (stdout, "\nFound:\n\t", frameCounter[0],
" sequences in reading frame 1\n\t",frameCounter[1],
" sequences in reading frame 2\n\t",frameCounter[2],
" sequences in reading frame 3\n\n",
"There were ", Abs(stillHasStops), " sequences with apparent frameshift/sequencing errors\n");
skipSeqs = {};
for (k=0; k<Abs(stillHasStops); k += 1)
{
seqCounter = stillHasStops[k];
seqName = sequenceNames[seqCounter];
fprintf (stdout,"Sequence ", seqCounter+1, " (", seqName, ") seems to have");
stopPosn = StopPositions[seqCounter];
fStart = -1;
fEnd = -1;
fMin = 1e10;
frame1 = 0;
frame2 = 0;
checkFramePosition (stopPosn[0][1],stopPosn[1][0],0,1);
checkFramePosition (stopPosn[1][1],stopPosn[0][0],1,0);
checkFramePosition (stopPosn[0][1],stopPosn[2][0],0,2);
checkFramePosition (stopPosn[2][1],stopPosn[0][0],2,0);
checkFramePosition (stopPosn[2][1],stopPosn[1][0],2,1);
checkFramePosition (stopPosn[1][1],stopPosn[2][0],1,2);
if (fStart>=0)
{
allTran = AllTranslations[seqCounter];
useq = UnalignedSeqs[seqCounter];
fprintf (stdout, " a shift from frame ", frame2+1, " to frame ", frame1+1, " between a.a. positions ", fStart, " and ", fEnd, ".");
fStart2 = Max(fStart-1,0);
fEnd2 = Min(fEnd+1,Min(Abs(allTran[frame1]),Abs(allTran[frame2]))-1);
tempString = allTran[frame2];
fprintf (stdout, "\n\tRegion ", fStart2, "-", fEnd2, " in frame ", frame2+1, ":\n\t", tempString[fStart2][fEnd2]);
fprintf (stdout, "\n\t", useq[3*fStart2+frame2][3*fEnd2+frame2-1]);
tempString = allTran[frame1];
fprintf (stdout, "\n\tRegion ", fStart2, "-", fEnd2, " in frame ", frame1+1, ":\n\t", tempString[fStart2][fEnd2]);
fprintf (stdout, "\n\t", useq[3*fStart2+frame1][3*fEnd2+frame1-1]);
fprintf (stdout, "\n\t\tAttempting to resolve by alignment to reference. ");
f1s = allTran[frame1];
f2s = allTran[frame2];
f1l = Abs(f1s);
bestScore = -1e10;
bestSplice = -1;
for (k2=fStart; k2<fEnd; k2=k2+1)
{
s2 = f2s[0][k2]+f1s[k2+1][Abs(f1s)];
inStr = {{s1,s2}};
AlignSequences(aligned, inStr, alignOptions);
aligned = aligned[0];
aligned = aligned[0];
if (aligned > bestScore)
{
bestScore = aligned;
bestSplice = k2;
bestString = s2;
}
}
fprintf (stdout, "Best splice site appears to be at a.a. position ", bestSplice, "\n");
/* update best spliced string */
ProteinSequences[seqCounter] = bestString;
ReadingFrames[seqCounter] = 0;
UnalignedSeqs[seqCounter] = useq[frame2][frame2+3*bestSplice+2] + useq[frame1+3*bestSplice+3][Abs(useq)-1] + "---";
}
else
{
fprintf (stdout, " multiple frameshifts\n");
skipSeqs[seqCounter] = 1;
}
}
SeqAlignments = {};
startingPosition = {unalSequenceCount,2};
refLength = Abs(ProteinSequences[0]);
refInsertions = {refLength+1,1};
fprintf (stdout,"\nPerforming pairwise alignment with reference sequences\n");
alignmentScores = {};
for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter += 1)
{
if (skipSeqs[seqCounter] == 0)
{
s2 = ProteinSequences[seqCounter];
inStr = {{s1,s2}};
AlignSequences(aligned, inStr, alignOptions);
aligned = aligned[0];
SeqAlignments[seqCounter] = aligned;
alignmentScores + aligned[0]/Abs(aligned[1]);
aligned = aligned[1];
myStartingPosition = aligned$"[^-]";
myEndingPosition = Abs (aligned)-1;
while (aligned[myEndingPosition]=="-")
{
myEndingPosition = myEndingPosition - 1;
}
myStartingPosition = myStartingPosition[0];
startingPosition[seqCounter][0] = myStartingPosition;
startingPosition[seqCounter][1] = myEndingPosition;
aligned = aligned[myStartingPosition][myEndingPosition];
refInsert = aligned||"-+";
if (refInsert[0]>0)
{
insCount = Rows (refInsert)/2;
offset = 0;
for (insN = 0; insN < insCount; insN = insN+1)
{
insPos = refInsert[insN*2];
insLength = refInsert[insN*2+1]-insPos+1;
insPos = insPos-offset;
if (refInsertions[insPos]<insLength)
{
refInsertions[insPos]=insLength;
}
offset = offset + insLength;
}
}
}
}
alignmentScoresM = avlToMatrix ("alignmentScores");
LoadFunctionLibrary ("DescriptiveStatistics.bf");
distInfo = GatherDescriptiveStats (alignmentScoresM);
distInfo["Mean"] - 2*distInfo["Std.Dev"];
fprintf (stdout,"\nMerging pairwise alignments into a MSA\n");
fullRefSeq = "";
fullRefSeq * refLength;
fullRefSeq * (s1[0]);
s1N = UnalignedSeqs[0];
fullRefSeqN = "";
fullRefSeqN * (3*refLength);
fullRefSeqN * (s1N[0][2]);
frameShift = ReadingFrames[0];
for (seqCounter=1;seqCounter<refLength;seqCounter=seqCounter+1)
{
gapCount = refInsertions[seqCounter];
for (k=0; k<gapCount;k=k+1)
{
fullRefSeq*("-");
fullRefSeqN*("---");
}
fullRefSeq * (s1[seqCounter]);
fullRefSeqN * (s1N[frameShift+seqCounter*3][frameShift+seqCounter*3+2]);
}
fullRefSeq * 0;
fullRefSeqN * 0;
refLength = Abs(fullRefSeq);
seqName=sequenceNames[0];
if (writeToFiles)
{
SetDialogPrompt ("Save alignment to:");
fprintf (PROMPT_FOR_FILE,CLEAR_FILE,">",seqName,"\n",fullRefSeq);
fName = LAST_FILE_PATH;
fNameC = fName+".nuc";
fprintf (fNameC,CLEAR_FILE,">",seqName,"\n",fullRefSeqN);
}
else
{
result [seqName] = fullRefSeqN;
}
alCounter = 0;
for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter += 1)
{
if (skipSeqs[seqCounter] == 0)
{
if (skipOutliers == 0 && alignmentScoresM[alCounter] < lowerCuttoff)
{
seqName=sequenceNames[seqCounter];
fprintf (stdout, "Sequence ", seqName ," was skipped because of a poor alignment score.\n");
skipSeqs[seqCounter] = 1;
alCounter = alCounter + 1;
continue;
}
alCounter = alCounter + 1;
seqName=sequenceNames[seqCounter];
aligned = SeqAlignments[seqCounter];
aligned1 = aligned[1];
aligned2 = aligned[2];
s2 = startingPosition[seqCounter][0];
e2 = startingPosition[seqCounter][1];
gappedSeq = "";
gappedSeq * Abs(aligned2);
k=0;
while (k<refLength)
{
while (fullRefSeq[k]!=aligned1[s2])
{
gappedSeq*("-");
k=k+1;
}
gappedSeq*(aligned2[s2]);
s2=s2+1;
k=k+1;
}
gappedSeq * 0;
gappedSeqN = "";
gappedSeqN * (3*Abs(aligned2));
frameShift = ReadingFrames[seqCounter];
s1N = UnalignedSeqs[seqCounter];
s2N = ProteinSequences[seqCounter];
s2 = startingPosition[seqCounter][0];
k = 0;
e2 = Abs(gappedSeq);
k = 0;
while (k<e2)
{
while ((s2N[s2]!=gappedSeq[k])&&(k<e2))
{
gappedSeqN * ("---");
k=k+1;
}
if (k<e2)
{
gappedSeqN * s1N[frameShift+s2*3][frameShift+s2*3+2];
s2 = s2+1;
k=k+1;
}
}
gappedSeqN * 0;
if (writeToFiles)
{
if (refSeq2 && seqCounter == unalSequenceCount-1)
{
fscanf (fName, "Raw", soFar);
fprintf (fName, CLEAR_FILE,">",seqName,"\n",gappedSeq,"\n",soFar);
fscanf (fNameC, "Raw", soFar);
fprintf (fNameC,CLEAR_FILE,">",seqName,"\n",gappedSeqN,"\n",soFar);
}
else
{
fprintf (fName,"\n>",seqName,"\n",gappedSeq);
fprintf (fNameC,"\n>",seqName,"\n",gappedSeqN);
}
}
else
{
result [seqName] = gappedSeqN;
}
}
}
if (Abs(skipSeqs) && writeToFiles)
{
fName = fName+".bad";
for (seqCounter = 1; seqCounter < unalSequenceCount; seqCounter = seqCounter+1)
{
if (skipSeqs[seqCounter])
{
seqName=sequenceNames[seqCounter];
fprintf (fName,">",seqName,"\n",UnalignedSeqs[seqCounter],"\n");
}
}
}
return result;
}
//---------------------------------------------------------------------------------------------------------------------
function checkFramePosition (pos1, pos2, fr1, fr2)
{
fSpan = pos2-pos1;
if (fSpan>1) // first followed by second
{
if (fSpan < fMin)
{
fMin = fSpan;
frame1 = fr1;
frame2 = fr2;
fStart = pos1+1;
fEnd = pos2;
}
}
return 0;
}
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