diff --git a/Tests/SubsMat/aaDistrib.txt b/Tests/SubsMat/aaDistrib.txt
new file mode 100644
index 00000000000..86d1e83bb0b
--- /dev/null
+++ b/Tests/SubsMat/aaDistrib.txt
@@ -0,0 +1,20 @@
+A 2377 0.0852491
+C 383 0.013736
+D 1669 0.0598573
+E 1655 0.0593552
+F 1167 0.0418535
+G 2185 0.0783632
+H 627 0.0224868
+I 1455 0.0521823
+K 1614 0.0578847
+L 2360 0.0846394
+M 651 0.0233476
+N 1387 0.0497436
+P 1191 0.0427142
+Q 1022 0.0366532
+R 1282 0.0459778
+S 1664 0.0596779
+T 1599 0.0573468
+V 2052 0.0735932
+W 421 0.0150988
+Y 1119 0.040132
diff --git a/Tests/SubsMat/acc_rep_mat.pik b/Tests/SubsMat/acc_rep_mat.pik
new file mode 100644
index 00000000000..1d5c34fbc16
--- /dev/null
+++ b/Tests/SubsMat/acc_rep_mat.pik
@@ -0,0 +1,632 @@
+(dp1
+(S'L'
+S'R'
+tI109
+s(S'I'
+S'I'
+tI145
+s(S'Q'
+S'Q'
+tI42
+s(S'S'
+S'T'
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+s(S'H'
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+tI69
+s(S'Q'
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+tI41
+s(S'H'
+S'P'
+tI23
+s(S'N'
+S'Y'
+tI75
+s(S'H'
+S'L'
+tI70
+s(S'D'
+S'K'
+tI169
+s(S'H'
+S'H'
+tI56
+s(S'N'
+S'Q'
+tI77
+s(S'T'
+S'Y'
+tI91
+s(S'L'
+S'N'
+tI101
+s(S'G'
+S'V'
+tI131
+s(S'G'
+S'R'
+tI81
+s(S'E'
+S'S'
+tI143
+s(S'E'
+S'W'
+tI21
+s(S'E'
+S'K'
+tI164
+s(S'Y'
+S'Y'
+tI82
+s(S'G'
+S'N'
+tI147
+s(S'E'
+S'G'
+tI146
+s(S'A'
+S'D'
+tI171
+s(S'C'
+S'C'
+tI42
+s(S'M'
+S'R'
+tI40
+s(S'P'
+S'T'
+tI92
+s(S'C'
+S'G'
+tI39
+s(S'M'
+S'V'
+tI95
+s(S'P'
+S'P'
+tI120
+s(S'I'
+S'T'
+tI88
+s(S'C'
+S'K'
+tI24
+s(S'L'
+S'V'
+tI447
+s(S'A'
+S'H'
+tI66
+s(S'K'
+S'W'
+tI21
+s(S'I'
+S'L'
+tI348
+s(S'C'
+S'S'
+tI23
+s(S'A'
+S'P'
+tI119
+s(S'L'
+S'T'
+tI183
+s(S'V'
+S'Y'
+tI134
+s(S'R'
+S'W'
+tI23
+s(S'G'
+S'W'
+tI35
+s(S'T'
+S'V'
+tI145
+s(S'M'
+S'N'
+tI34
+s(S'F'
+S'Q'
+tI39
+s(S'F'
+S'Y'
+tI142
+s(S'D'
+S'R'
+tI115
+s(S'D'
+S'V'
+tI95
+s(S'C'
+S'W'
+tI8
+s(S'D'
+S'N'
+tI163
+s(S'F'
+S'I'
+tI151
+s(S'F'
+S'M'
+tI67
+s(S'D'
+S'F'
+tI63
+s(S'S'
+S'S'
+tI116
+s(S'L'
+S'Q'
+tI79
+s(S'S'
+S'W'
+tI22
+s(S'Q'
+S'R'
+tI73
+s(S'N'
+S'N'
+tI66
+s(S'H'
+S'W'
+tI13
+s(S'L'
+S'Y'
+tI173
+s(S'H'
+S'S'
+tI59
+s(S'V'
+S'W'
+tI44
+s(S'H'
+S'K'
+tI63
+s(S'N'
+S'R'
+tI90
+s(S'L'
+S'M'
+tI153
+s(S'N'
+S'V'
+tI93
+s(S'A'
+S'S'
+tI199
+s(S'Q'
+S'W'
+tI15
+s(S'G'
+S'Q'
+tI89
+s(S'E'
+S'P'
+tI91
+s(S'E'
+S'T'
+tI150
+s(S'G'
+S'Y'
+tI101
+s(S'E'
+S'H'
+tI38
+s(S'R'
+S'S'
+tI94
+s(S'E'
+S'L'
+tI133
+s(S'G'
+S'M'
+tI49
+s(S'G'
+S'I'
+tI92
+s(S'P'
+S'W'
+tI18
+s(S'A'
+S'I'
+tI202
+s(S'A'
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+tI229
+s(S'P'
+S'S'
+tI103
+s(S'C'
+S'D'
+tI15
+s(S'A'
+S'C'
+tI49
+s(S'A'
+S'L'
+tI307
+s(S'K'
+S'P'
+tI94
+s(S'I'
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+tI38
+s(S'K'
+S'T'
+tI140
+s(S'A'
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+tI191
+s(S'C'
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+tI21
+s(S'A'
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+tI47
+s(S'Q'
+S'V'
+tI69
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+tI112
+s(S'V'
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+tI239
+s(S'R'
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+tI114
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+tI22
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+tI64
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+tI57
+s(S'F'
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+tI160
+s(S'D'
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+tI116
+s(S'K'
+S'Q'
+tI108
+s(S'D'
+S'I'
+tI66
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+tI20
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+tI79
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+tI22
+s(S'D'
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+tI163
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+tI55
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+tI94
+s(S'L'
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+tI79
+s(S'S'
+S'V'
+tI114
+s(S'Q'
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+tI101
+s(S'H'
+S'V'
+tI54
+s(S'I'
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+tI65
+s(S'I'
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+tI84
+s(S'H'
+S'R'
+tI44
+s(S'H'
+S'N'
+tI57
+s(S'N'
+S'S'
+tI115
+s(S'N'
+S'W'
+tI29
+s(S'L'
+S'L'
+tI320
+s(S'E'
+S'Y'
+tI60
+s(S'G'
+S'T'
+tI153
+s(S'G'
+S'P'
+tI108
+s(S'E'
+S'Q'
+tI105
+s(S'K'
+S'N'
+tI139
+s(S'E'
+S'I'
+tI63
+s(S'E'
+S'M'
+tI33
+s(S'G'
+S'L'
+tI154
+s(S'E'
+S'E'
+tI119
+s(S'G'
+S'H'
+tI53
+s(S'M'
+S'P'
+tI20
+s(S'P'
+S'V'
+tI109
+s(S'A'
+S'F'
+tI122
+s(S'K'
+S'Y'
+tI66
+s(S'M'
+S'T'
+tI35
+s(S'P'
+S'R'
+tI72
+s(S'C'
+S'E'
+tI26
+s(S'A'
+S'N'
+tI139
+s(S'C'
+S'I'
+tI42
+s(S'I'
+S'R'
+tI58
+s(S'C'
+S'M'
+tI14
+s(S'I'
+S'P'
+tI67
+s(S'A'
+S'V'
+tI252
+s(S'C'
+S'Q'
+tI16
+s(S'R'
+S'Y'
+tI62
+s(S'A'
+S'R'
+tI152
+s(S'K'
+S'M'
+tI32
+s(S'M'
+S'Y'
+tI41
+s(S'C'
+S'Y'
+tI19
+s(S'T'
+S'T'
+tI84
+s(S'F'
+S'S'
+tI92
+s(S'I'
+S'K'
+tI80
+s(S'C'
+S'L'
+tI62
+s(S'F'
+S'W'
+tI43
+s(S'A'
+S'T'
+tI195
+s(S'D'
+S'P'
+tI105
+s(S'D'
+S'T'
+tI125
+s(S'D'
+S'H'
+tI52
+s(S'F'
+S'G'
+tI102
+s(S'D'
+S'L'
+tI120
+s(S'F'
+S'K'
+tI67
+s(S'D'
+S'D'
+tI151
+s(S'Q'
+S'T'
+tI97
+s(S'C'
+S'H'
+tI10
+s(S'L'
+S'W'
+tI74
+s(S'H'
+S'Y'
+tI43
+s(S'S'
+S'Y'
+tI73
+s(S'H'
+S'Q'
+tI44
+s(S'W'
+S'W'
+tI32
+s(S'H'
+S'M'
+tI16
+s(S'H'
+S'I'
+tI31
+s(S'N'
+S'P'
+tI94
+s(S'N'
+S'T'
+tI105
+s(S'I'
+S'V'
+tI310
+s(S'G'
+S'S'
+tI161
+s(S'E'
+S'R'
+tI118
+s(S'W'
+S'Y'
+tI51
+s(S'E'
+S'V'
+tI110
+s(S'G'
+S'G'
+tI321
+s(S'E'
+S'N'
+tI115
+s(S'G'
+S'K'
+tI148
+s(S'E'
+S'F'
+tI50
+s(S'A'
+S'E'
+tI207
+s(S'C'
+S'N'
+tI24
+s(S'M'
+S'S'
+tI41
+s(S'C'
+S'F'
+tI32
+s(S'A'
+S'A'
+tI211
+s(S'P'
+S'Q'
+tI68
+s(S'M'
+S'W'
+tI25
+s(S'K'
+S'R'
+tI151
+s(S'A'
+S'M'
+tI79
+s(S'K'
+S'V'
+tI131
+s(S'I'
+S'Q'
+tI62
+s(S'P'
+S'Y'
+tI60
+s(S'C'
+S'R'
+tI15
+s(S'I'
+S'M'
+tI88
+s(S'C'
+S'V'
+tI59
+s(S'A'
+S'Q'
+tI129
+s(S'K'
+S'S'
+tI144
+s(S'M'
+S'Q'
+tI27
+s(S'R'
+S'V'
+tI88
+s(S'T'
+S'W'
+tI35
+s(S'A'
+S'Y'
+tI124
+s(S'R'
+S'R'
+tI96
+s(S'F'
+S'P'
+tI50
+s(S'C'
+S'T'
+tI30
+s(S'F'
+S'T'
+tI69
+s(S'D'
+S'S'
+tI167
+s(S'K'
+S'K'
+tI121
+s(S'L'
+S'S'
+tI159
+s(S'F'
+S'H'
+tI39
+s(S'D'
+S'G'
+tI143
+s(S'F'
+S'L'
+tI236
+s.
\ No newline at end of file
diff --git a/Tests/SubsMat/protein_count.txt b/Tests/SubsMat/protein_count.txt
new file mode 100644
index 00000000000..af58d787148
--- /dev/null
+++ b/Tests/SubsMat/protein_count.txt
@@ -0,0 +1,20 @@
+A 2377
+C 383
+D 1669
+E 1655
+F 1167
+G 2185
+H 627
+I 1455
+K 1614
+L 2360
+M 651
+N 1387
+P 1191
+Q 1022
+R 1282
+S 1664
+T 1599
+V 2052
+W 421
+Y 1119
diff --git a/Tests/SubsMat/protein_freq.txt b/Tests/SubsMat/protein_freq.txt
new file mode 100644
index 00000000000..ca6c30ba1d7
--- /dev/null
+++ b/Tests/SubsMat/protein_freq.txt
@@ -0,0 +1,20 @@
+A 0.0852491
+C 0.013736
+D 0.0598573
+E 0.0593552
+F 0.0418535
+G 0.0783632
+H 0.0224868
+I 0.0521823
+K 0.0578847
+L 0.0846394
+M 0.0233476
+N 0.0497436
+P 0.0427142
+Q 0.0366532
+R 0.0459778
+S 0.0596779
+T 0.0573468
+V 0.0735932
+W 0.0150988
+Y 0.040132
diff --git a/Tests/SubsMat/redAADistrib.txt b/Tests/SubsMat/redAADistrib.txt
new file mode 100644
index 00000000000..36e126de33c
--- /dev/null
+++ b/Tests/SubsMat/redAADistrib.txt
@@ -0,0 +1,7 @@
+F 9278 0.332748
+R 3334 0.119571
+O 5672 0.203422
+T 2896 0.103862
+N 3324 0.119212
+G 2185 0.0783632
+P 1191 0.0427142
diff --git a/Tests/SubsMat/redAltAADistrib.txt b/Tests/SubsMat/redAltAADistrib.txt
new file mode 100644
index 00000000000..f0bfd09442e
--- /dev/null
+++ b/Tests/SubsMat/redAltAADistrib.txt
@@ -0,0 +1,8 @@
+A 3411 0.2104153
+F 5867 0.1223327
+R 3334 0.119571
+O 5672 0.203422
+T 2896 0.103862
+N 3324 0.119212
+G 2185 0.0783632
+P 1191 0.0427142
diff --git a/Tests/output/test_SubsMat b/Tests/output/test_SubsMat
new file mode 100644
index 00000000000..622fcfbb972
--- /dev/null
+++ b/Tests/output/test_SubsMat
@@ -0,0 +1,1140 @@
+test_SubsMat
+Check differences between derived and true frequencies for each
+letter. Differences should be very small
+A 0.000009
+C 0.000001
+D 0.000006
+E 0.000006
+F 0.000004
+G 0.000008
+H 0.000002
+I 0.000006
+K 0.000006
+L 0.000009
+M 0.000002
+N 0.000005
+P 0.000005
+Q 0.000004
+R 0.000005
+S 0.000006
+T 0.000006
+V 0.000008
+W 0.000002
+Y 0.000004
+A 0.011
+C 0.002 0.002
+D 0.009 0.001 0.008
+E 0.010 0.001 0.008 0.006
+F 0.006 0.002 0.003 0.003 0.004
+G 0.011 0.002 0.007 0.007 0.005 0.016
+H 0.003 0.001 0.003 0.002 0.002 0.003 0.003
+I 0.010 0.002 0.003 0.003 0.008 0.005 0.002 0.007
+K 0.010 0.001 0.008 0.008 0.003 0.007 0.003 0.004 0.006
+L 0.015 0.003 0.006 0.007 0.012 0.008 0.004 0.017 0.006 0.016
+M 0.004 0.001 0.001 0.002 0.003 0.002 0.001 0.004 0.002 0.008 0.001
+N 0.007 0.001 0.008 0.006 0.003 0.007 0.003 0.003 0.007 0.005 0.002 0.003
+P 0.006 0.001 0.005 0.005 0.003 0.005 0.001 0.003 0.005 0.004 0.001 0.005 0.006
+Q 0.006 0.001 0.006 0.005 0.002 0.004 0.002 0.003 0.005 0.004 0.001 0.004 0.003 0.002
+R 0.008 0.001 0.006 0.006 0.003 0.004 0.002 0.003 0.008 0.005 0.002 0.005 0.004 0.004 0.005
+S 0.010 0.001 0.008 0.007 0.005 0.008 0.003 0.004 0.007 0.008 0.002 0.006 0.005 0.005 0.005 0.006
+T 0.010 0.002 0.006 0.008 0.003 0.008 0.003 0.004 0.007 0.009 0.002 0.005 0.005 0.005 0.006 0.009 0.004
+V 0.013 0.003 0.005 0.006 0.008 0.007 0.003 0.016 0.007 0.022 0.005 0.005 0.005 0.003 0.004 0.006 0.007 0.012
+W 0.002 0.000 0.001 0.001 0.002 0.002 0.001 0.002 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.002
+Y 0.006 0.001 0.003 0.003 0.007 0.005 0.002 0.005 0.003 0.009 0.002 0.004 0.003 0.002 0.003 0.004 0.005 0.007 0.003 0.004
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+Diff between supplied and matrix-derived frequencies, should be small
+Y 0.00
+V 0.00
+W 0.00
+T 0.00
+R 0.00
+S 0.00
+P 0.00
+Q 0.00
+N 0.00
+L 0.01
+M 0.00
+K 0.00
+H 0.00
+I 0.01
+F 0.00
+G 0.01
+D 0.00
+E 0.00
+C 0.00
+A 0.00
+Calculating sum of letters for an observed frequency matrix
+Y	0.04
+V	0.08
+W	0.02
+T	0.06
+R	0.04
+S	0.06
+P	0.04
+Q	0.04
+N	0.05
+L	0.09
+M	0.02
+K	0.06
+H	0.02
+I	0.06
+F	0.04
+G	0.07
+D	0.06
+E	0.05
+C	0.02
+A	0.09
+Total sum 1.00 should be 1.0
+
+Log odds matrix
+A 1.60
+V -0.20 2.90
+I 0.10 2.30 3.30
+L -0.20 1.90 2.10 2.60
+M -0.10 1.10 2.00 2.30 2.90
+C -0.30 0.90 0.70 0.30 -0.20 9.50
+F -1.00 0.60 1.60 1.50 1.90 0.70 2.90
+W -0.70 -0.60 0.00 0.90 2.10 -0.90 1.70 7.80
+Y -0.60 0.10 -0.20 0.40 0.10 -1.30 2.80 2.70 3.70
+H -0.90 -1.40 -2.50 -1.10 -1.50 -1.70 -0.40 -0.80 0.30 6.90
+S 0.10 -2.00 -2.00 -1.30 -1.30 -1.80 -0.50 -2.30 -1.20 0.30 2.40
+T 0.10 -0.80 -1.70 -0.60 -1.90 -0.60 -1.70 -0.20 -0.20 1.10 1.20 1.20
+N -0.50 -1.90 -2.20 -2.30 -1.10 -0.70 -1.80 -0.10 -0.20 1.10 0.30 0.00 1.90
+Q 0.20 -2.10 -1.30 -2.30 -1.00 -1.40 -2.20 -1.90 -1.70 1.10 0.90 0.80 0.60 2.10
+K -0.10 -1.30 -2.20 -2.80 -2.30 -1.60 -1.90 -2.50 -1.60 0.60 0.40 0.40 1.20 1.20 2.70
+R 0.10 -1.90 -2.40 -1.80 -0.20 -2.50 -1.40 -0.90 -0.70 0.20 -0.30 0.60 0.50 0.60 1.80 4.00
+D -0.50 -2.70 -3.00 -2.50 -4.30 -3.60 -2.10 -2.20 -1.70 -0.20 1.10 -0.10 1.90 1.50 1.20 0.70 3.70
+E 0.50 -1.90 -3.00 -1.80 -2.00 -1.10 -2.90 -2.20 -1.80 -1.40 0.60 0.90 0.60 1.30 1.20 0.90 1.20 3.00
+G -0.20 -2.20 -2.50 -2.30 -1.30 -0.40 -0.90 -1.10 -0.70 -1.00 -0.00 -0.10 0.50 -0.50 -0.30 -1.80 -0.40 -0.20 5.10
+P -0.70 -0.70 -1.50 -2.90 -2.90 -0.80 -1.70 -1.70 -0.60 -2.30 0.40 -0.00 0.90 0.60 0.00 0.00 0.60 0.10 -0.30 5.60
+   A   V   I   L   M   C   F   W   Y   H   S   T   N   Q   K   R   D   E   G   P
+
+Testing MatrixInfo
+
+benner6
+------------
+A   2
+C  -1  12
+D   0  -3   5
+E   0  -4   4   5
+F  -3   0  -5  -6   8
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+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+benner22
+------------
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+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+benner74
+------------
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+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+blosum100
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum30
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum35
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum40
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum45
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum50
+------------
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+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+blosum55
+------------
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+
+blosum60
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+
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+
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+
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+
+blosum75
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+
+blosum80
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+
+blosum85
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+
+blosum90
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+
+blosum95
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+W  -4  -6  -4  -6  -5   0  -5  -3  -4  -5  -3  -2  -5  -5  -3  -4  -4  -4  -3  11
+X  -1  -2  -3  -2  -2  -2  -3  -2  -2  -1  -2  -2  -2  -3  -1  -2  -1  -1  -2  -4  -2
+Y  -3  -4  -4  -5  -4   3  -5   1  -2  -3  -2  -3  -3  -5  -3  -3  -3  -3  -3   2  -2   8
+Z  -1   0  -5   0   4  -4  -3   0  -4   0  -4  -2  -1  -2   4  -1  -1  -2  -3  -4  -1  -4   4
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+feng
+------------
+A   6
+C   2   6
+D   4   1   6
+E   4   0   5   6
+F   2   3   1   0   6
+G   5   3   4   4   1   6
+H   2   2   3   2   2   1   6
+I   2   2   1   1   4   2   1   6
+K   3   0   3   4   0   2   3   2   6
+L   2   2   1   1   4   2   3   5   2   6
+M   2   2   0   1   2   1   1   4   2   5   6
+N   3   2   5   3   1   3   4   2   4   1   1   6
+P   5   2   2   3   2   3   3   2   2   3   2   2   6
+Q   3   1   4   4   1   2   4   1   4   2   2   3   3   6
+R   2   2   2   2   1   3   4   2   5   2   2   2   3   3   6
+S   5   4   3   3   3   5   3   2   3   2   1   5   4   3   3   6
+T   5   2   2   3   1   2   2   3   4   2   3   4   4   3   3   5   6
+V   5   2   3   4   4   4   1   5   3   5   4   2   3   2   2   2   3   6
+W   2   3   0   1   3   3   1   2   1   4   3   0   2   1   2   2   1   3   6
+Y   2   3   2   1   5   2   3   3   1   3   2   3   2   2   1   3   2   3   3   6
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+fitch
+------------
+A   3
+C   1   3
+E   1   1   3
+F   1   2   1   3
+H   2   1   1   1   3
+I   1   0   2   0   1   3
+L   2   1   2   1   1   1   3
+M   0   0   2   1   0   2   1   3
+N   2   1   2   1   2   2   1   1   3
+O   2   2   1   2   2   1   1   0   2   3
+Q   1   1   1   1   2   2   1   1   1   2   3
+R   1   2   2   1   2   2   1   2   1   1   2   3
+S   1   2   2   2   1   1   2   1   2   2   2   2   3
+T   0   2   1   1   0   1   1   1   0   1   2   2   2   3
+U   1   1   1   2   2   1   1   2   1   1   2   2   2   2   3
+V   2   2   1   2   1   1   2   2   1   1   1   1   1   1   2   3
+W   1   1   2   2   1   1   1   2   2   1   0   1   2   0   2   2   3
+Y   2   2   1   1   1   1   2   1   1   1   1   2   2   2   2   2   1   3
+   A   C   E   F   H   I   L   M   N   O   Q   R   S   T   U   V   W   Y
+
+genetic
+------------
+A   4
+C  -1   5
+D   1  -1   4
+E   1  -3   3   5
+F  -2   1  -1  -2   4
+G   1   1   1   1  -1   4
+H  -2  -1   1   0  -1  -2   4
+I  -1  -1  -2  -2   1  -2  -1   4
+K  -1  -3   0   2  -2  -2   0   0   5
+L  -2  -1  -2  -2   2  -2   0   1  -2   3
+M  -2  -2  -2  -1   0  -2  -1   3   1   1   5
+N  -1  -1   1   0  -1  -2   1   0   3  -2   0   4
+P   0  -1  -2  -2  -1  -1   0  -1  -1   0  -1  -1   3
+Q  -2  -3   0   2  -2  -2   3  -1   2   0  -1   0   1   5
+R  -1   0  -2  -2  -1   0   3  -1   0   0   0  -1   0   0   2
+S   0   1  -2  -2   0   0  -1   0  -1  -1  -1   0   0  -2   0   2
+T   0  -1  -2  -2  -2  -2  -1   0   1  -1   0   0   1  -1   0   1   4
+V   1  -2   1   1   1   1  -2   1  -2   1   1  -2  -2  -2  -2  -2  -2   4
+W  -2   4  -2  -3   0   1  -2  -2  -3   0  -2  -3  -1  -2   1   0  -2  -2   7
+Y  -2   2   2   0   2  -1   2  -1   0  -1  -2   2  -2   0  -1   0  -2  -2   0   6
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+gonnet
+------------
+A   2
+C   0  11
+D   0  -3   4
+E   0  -3   2   3
+F  -2   0  -4  -3   7
+G   0  -2   0   0  -5   6
+H   0  -1   0   0   0  -1   6
+I   0  -1  -3  -2   1  -4  -2   4
+K   0  -2   0   1  -3  -1   0  -2   3
+L  -1  -1  -4  -2   2  -4  -1   2  -2   4
+M   0   0  -3  -2   1  -3  -1   2  -1   2   4
+N   0  -1   2   0  -3   0   1  -2   0  -3  -2   3
+P   0  -3   0   0  -3  -1  -1  -2   0  -2  -2   0   7
+Q   0  -2   0   1  -2  -1   1  -1   1  -1  -1   0   0   2
+R   0  -2   0   0  -3  -1   0  -2   2  -2  -1   0   0   1   4
+S   1   0   0   0  -2   0   0  -1   0  -2  -1   0   0   0   0   2
+T   0   0   0   0  -2  -1   0   0   0  -1   0   0   0   0   0   1   2
+V   0   0  -2  -1   0  -3  -2   3  -1   1   1  -2  -1  -1  -2  -1   0   3
+W  -3  -1  -5  -4   3  -4   0  -1  -3   0  -1  -3  -5  -2  -1  -3  -3  -2  14
+Y  -2   0  -2  -2   5  -4   2   0  -2   0   0  -1  -3  -1  -1  -1  -1  -1   4   7
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+grant
+------------
+A 215
+C  61 215
+E 130  66 215
+F  38  10 112 215
+G 170  45 150  75 215
+H 134  41 168 115 175 215
+I 114  13 137 113 159 183 215
+L  89  20 157 102 108 129 109 215
+M  55  19 134 187  89 128 120 131 215
+N 192  76 150  57 173 147 121 104  73 215
+O  55  21 123 193  93 132 130 103 179  72 215
+P 107  46 177 101 122 138 112 188 128 124 105 215
+Q 154  61 173  99 186 191 162 124 114 169 116 139 215
+R 119  35 144 118 161 186 189 103 124 129 138 112 172 215
+S 150 103 157  60 135 126  94 116  80 169  71 141 147 105 215
+T  34   0  87 175  63 100 105  67 148  41 178  68  85 114  38 215
+U  43  17 123 193  77 116 108 119 200  62 179 117 102 113  70 154 215
+V  63  23 146 165  94 131 118 151 194  82 160 147 119 119  91 127 183 215
+W  47  17 126 194  81 121 113 121 205  66 182 120 106 118  73 154 210 186 215
+Y 121  56 156  62 117 117  88 155  88 135  68 173 128  90 159  31  77 106  80 215
+   A   C   E   F   G   H   I   L   M   N   O   P   Q   R   S   T   U   V   W   Y
+
+ident
+------------
+A   6
+C  -1   6
+D  -1  -1   6
+E  -1  -1  -1   6
+F  -1  -1  -1  -1   6
+G  -1  -1  -1  -1  -1   6
+H  -1  -1  -1  -1  -1  -1   6
+I  -1  -1  -1  -1  -1  -1  -1   6
+K  -1  -1  -1  -1  -1  -1  -1  -1   6
+L  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+M  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+N  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+P  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+Q  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+R  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+S  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+T  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+V  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+W  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+Y  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1   6
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+johnson
+------------
+A   6
+C  -3  16
+D  -1  -9   8
+E   0  -6   2   8
+F  -3  -4  -7  -6  10
+G   0  -8  -2  -2  -8   8
+H  -3  -8   0  -2  -1  -3  12
+I  -2  -7  -4  -4   0  -5  -5   8
+K   0  -8  -1   1  -5  -3   0  -4   7
+L  -3  -8  -8  -5   1  -7  -4   2  -3   7
+M  -1  -4  -5  -2   0  -5  -2   2  -1   4  11
+N  -1  -7   2   0  -3  -1   1  -4   0  -4  -3   8
+P  -1  -8  -1  -1  -5  -2  -4  -5   0  -2  -9  -2  10
+Q   0  -6  -1   2  -6  -2   1  -7   1  -4   0   0  -3   9
+R  -1  -5  -3   0  -6  -2   0  -5   3  -3  -4  -1  -3   2  10
+S   0  -7   0  -2  -4  -1  -2  -4  -1  -5  -4   1  -1  -1   0   5
+T   0  -6  -1   0  -5  -3  -3  -3   0  -4  -3   0  -2   0  -1   2   6
+V   0  -4  -5  -4  -1  -5  -3   3  -3   1   0  -5  -5  -3  -4  -4  -1   7
+W  -5  -9  -6  -7   3  -6  -4  -3  -5  -1   0  -6  -7  -8  -3  -6  -9  -4  15
+Y  -4  -7  -3  -3   3  -5   0  -2  -3  -2  -1  -1  -7  -5  -2  -3  -2  -1   2  10
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+levin
+------------
+A   2
+C   0   2
+D   0   0   2
+E   1   0   1   2
+F  -1  -1  -1  -1   2
+G   0   0   0   0  -1   2
+H   0   0   0   0  -1   0   2
+I   0   0  -1  -1   1  -1  -1   2
+K   0   0   0   0  -1   0   0  -1   2
+L   0   0  -1  -1   0  -1  -1   0  -1   2
+M   0   0  -1  -1   0  -1  -1   0  -1   2   2
+N   0   0   1   0  -1   0   0  -1   1  -1  -1   3
+P  -1   0   0  -1  -1   0   0  -1   0  -1  -1   0   3
+Q   0   0   0   1  -1   0   0  -1   0  -1  -1   1   0   2
+R   0   0   0   0  -1   0   0  -1   1  -1  -1   0   0   0   2
+S   1   0   0   0  -1   0   0  -1   0  -1  -1   0   0   0   0   2
+T   0   0   0   0  -1   0   0   0   0   0   0   0   0   0   0   0   2
+V   0   0  -1  -1   0  -1  -1   1  -1   1   0  -1  -1  -1  -1  -1   0   2
+W  -1  -1  -1  -1   0  -1  -1   0  -1   0   0  -1  -1  -1   0  -1  -1   0   2
+Y  -1  -1  -1  -1   1  -1   0   0  -1   0   0  -1  -1  -1  -1  -1  -1   0   0   2
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+mclach
+------------
+A   8
+C   1   9
+D   3   1   8
+E   4   0   5   8
+F   1   0   1   0   9
+G   3   1   3   3   0   8
+H   3   3   4   2   4   2   8
+I   2   1   1   1   3   1   2   8
+K   3   0   3   4   0   3   4   1   8
+L   2   0   1   1   5   1   2   5   2   8
+M   3   3   2   1   5   1   3   5   1   6   8
+N   3   1   5   4   0   3   4   1   4   1   2   8
+P   4   0   3   4   1   3   3   1   3   1   1   1   8
+Q   3   0   4   5   0   2   4   0   4   3   3   4   3   8
+R   2   1   1   3   1   3   5   1   5   2   1   3   3   5   8
+S   4   2   3   4   2   3   3   2   3   2   2   5   3   4   4   8
+T   3   2   3   4   1   2   4   3   3   3   3   3   3   3   3   5   8
+V   3   1   1   2   3   2   2   5   2   5   4   1   2   2   2   2   3   8
+W   1   2   0   1   6   1   3   3   1   3   1   0   0   2   3   3   2   2   9
+Y   1   1   1   2   6   0   4   3   1   3   2   2   0   1   2   3   1   3   6   9
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+miyata
+------------
+A   1
+C   0   1
+D  -1  -2   1
+E  -1  -2   0   1
+F  -1   0  -3  -2   1
+G   0   0  -1  -1  -2   1
+H   0  -1   0   0  -1  -1   1
+I  -1   0  -2  -2   0  -2  -1   1
+K  -1  -2   0   0  -1  -2   0  -1   1
+L  -1   0  -2  -2   0  -2  -1   1  -1   1
+M  -1   0  -2  -1   0  -2   0   0  -1   0   1
+N   0  -1   0   0  -2   0   0  -2   0  -2  -1   1
+P   1   0  -1  -1  -1   0   0  -1  -1  -1  -1   0   1
+Q   0  -1   0   0  -1  -1   0  -1   0  -1  -1   0   0   1
+R  -1  -1  -1   0  -1  -2   0  -1   0  -1  -1   0  -1   0   1
+S   0   0   0   0  -2   0   0  -1  -1  -1  -1   0   0   0  -1   1
+T   0   0   0   0  -1   0   0   0   0  -1   0   0   0   0   0   0   1
+V   0   0  -2  -1   0  -1   0   0  -1   0   0  -1   0   0  -1   0   0   1
+W  -2  -2  -3  -2   0  -3  -1   0  -1   0   0  -3  -2  -2  -1  -3  -2  -1   1
+Y  -1  -1  -2  -1   0  -2  -1   0  -1   0   0  -2  -1  -1   0  -2  -1   0   0   1
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+nwsgappep
+------------
+A   1
+B   0   1
+C   0   0   1
+D   0   1   0   1
+E   0   0   0   1   1
+F   0   0   0  -1   0   1
+G   0   0   0   0   0   0   1
+H   0   0   0   0   0   0   0   1
+I   0   0   0   0   0   0   0   0   1
+K   0   0   0   0   0   0   0   0   0   1
+L   0   0   0   0   0   1   0   0   0   0   1
+M   0   0   0   0   0   0   0   0   0   0   1   1
+N   0   1   0   0   0   0   0   0   0   0   0   0   1
+P   0   0   0   0   0   0   0   0   0   0   0   0   0   1
+Q   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1
+R   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1
+S   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1
+T   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1
+V   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   1
+W   0   0  -1  -1  -1   1  -1   0   0   0   0   0   0   0   0   1   0   0   0   1
+Y   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1
+Z   0   0   0   0   1   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   1
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y   Z
+
+pam120
+------------
+A   3
+B   0   4
+C  -3  -6   9
+D   0   4  -7   5
+E   0   3  -7   3   5
+F  -4  -5  -6  -7  -7   8
+G   1   0  -4   0  -1  -5   5
+H  -3   1  -4   0  -1  -3  -4   7
+I  -1  -3  -3  -3  -3   0  -4  -4   6
+K  -2   0  -7  -1  -1  -7  -3  -2  -3   5
+L  -3  -4  -7  -5  -4   0  -5  -3   1  -4   5
+M  -2  -4  -6  -4  -3  -1  -4  -4   1   0   3   8
+N  -1   3  -5   2   1  -4   0   2  -2   1  -4  -3   4
+P   1  -2  -4  -3  -2  -5  -2  -1  -3  -2  -3  -3  -2   6
+Q  -1   0  -7   1   2  -6  -3   3  -3   0  -2  -1   0   0   6
+R  -3  -2  -4  -3  -3  -5  -4   1  -2   2  -4  -1  -1  -1   1   6
+S   1   0   0   0  -1  -3   1  -2  -2  -1  -4  -2   1   1  -2  -1   3
+T   1   0  -3  -1  -2  -4  -1  -3   0  -1  -3  -1   0  -1  -2  -2   2   4
+V   0  -3  -3  -3  -3  -3  -2  -3   3  -4   1   1  -3  -2  -3  -3  -2   0   5
+W  -7  -6  -8  -8  -8  -1  -8  -3  -6  -5  -3  -6  -4  -7  -6   1  -2  -6  -8  12
+X  -1  -1  -4  -2  -1  -3  -2  -2  -1  -2  -2  -2  -1  -2  -1  -2  -1  -1  -1  -5  -2
+Y  -4  -3  -1  -5  -5   4  -6  -1  -2  -5  -2  -4  -2  -6  -5  -5  -3  -3  -3  -2  -3   8
+Z  -1   2  -7   3   4  -6  -2   1  -3  -1  -3  -2   0  -1   4  -1  -1  -2  -3  -7  -1  -5   4
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam180
+------------
+A   3
+B   0   4
+C  -3  -6  13
+D   0   4  -7   5
+E   0   3  -7   4   5
+F  -5  -6  -6  -8  -7  10
+G   1   0  -5   0   0  -6   6
+H  -2   1  -4   0   0  -3  -3   8
+I  -1  -3  -3  -3  -3   1  -4  -4   6
+K  -2   0  -7   0  -1  -7  -3  -1  -3   6
+L  -3  -5  -8  -6  -5   1  -6  -3   2  -4   7
+M  -2  -3  -7  -4  -3   0  -4  -3   2   1   4   9
+N   0   3  -5   3   2  -5   0   2  -3   1  -4  -3   4
+P   1  -2  -4  -2  -1  -6  -1  -1  -3  -2  -4  -3  -1   8
+Q  -1   1  -7   2   3  -6  -2   4  -3   0  -2  -1   0   0   6
+R  -3  -2  -5  -3  -2  -6  -4   2  -3   4  -4  -1  -1  -1   1   8
+S   1   1   0   0  -1  -4   1  -2  -2  -1  -4  -2   1   1  -1  -1   3
+T   2   0  -3  -1  -1  -4  -1  -2   0   0  -3  -1   0   0  -2  -2   2   4
+V   0  -3  -3  -3  -3  -2  -2  -3   5  -4   2   2  -3  -2  -3  -4  -2   0   6
+W  -8  -7 -10  -9  -9   0  -9  -4  -7  -5  -3  -6  -5  -7  -6   2  -3  -7  -8  18
+X  -1  -1  -4  -1  -1  -3  -2  -1  -1  -1  -2  -1  -1  -1  -1  -2   0  -1  -1  -6  -1
+Y  -5  -4   0  -6  -6   7  -7   0  -2  -6  -2  -4  -2  -7  -6  -6  -4  -4  -4  -1  -3  11
+Z   0   3  -7   3   5  -7  -1   2  -3   0  -3  -2   1  -1   5   0  -1  -1  -3  -8  -1  -6   5
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam250
+------------
+A   2
+B   0   3
+C  -2  -4  12
+D   0   3  -5   4
+E   0   3  -5   3   4
+F  -3  -4  -4  -6  -5   9
+G   1   0  -3   1   0  -5   5
+H  -1   1  -3   1   1  -2  -2   6
+I  -1  -2  -2  -2  -2   1  -3  -2   5
+K  -1   1  -5   0   0  -5  -2   0  -2   5
+L  -2  -3  -6  -4  -3   2  -4  -2   2  -3   6
+M  -1  -2  -5  -3  -2   0  -3  -2   2   0   4   6
+N   0   2  -4   2   1  -3   0   2  -2   1  -3  -2   2
+P   1  -1  -3  -1  -1  -5   0   0  -2  -1  -3  -2   0   6
+Q   0   1  -5   2   2  -5  -1   3  -2   1  -2  -1   1   0   4
+R  -2  -1  -4  -1  -1  -4  -3   2  -2   3  -3   0   0   0   1   6
+S   1   0   0   0   0  -3   1  -1  -1   0  -3  -2   1   1  -1   0   2
+T   1   0  -2   0   0  -3   0  -1   0   0  -2  -1   0   0  -1  -1   1   3
+V   0  -2  -2  -2  -2  -1  -1  -2   4  -2   2   2  -2  -1  -2  -2  -1   0   4
+W  -6  -5  -8  -7  -7   0  -7  -3  -5  -3  -2  -4  -4  -6  -5   2  -2  -5  -6  17
+X   0  -1  -3  -1  -1  -2  -1  -1  -1  -1  -1  -1   0  -1  -1  -1   0   0  -1  -4  -1
+Y  -3  -3   0  -4  -4   7  -5   0  -1  -4  -1  -2  -2  -5  -4  -4  -3  -3  -2   0  -2  10
+Z   0   2  -5   3   3  -5   0   2  -2   0  -3  -2   1   0   3   0   0  -1  -2  -6  -1  -4   3
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam30
+------------
+A   6
+B  -3   6
+C  -6 -12  10
+D  -3   6 -14   8
+E  -2   1 -14   2   8
+F  -8 -10 -13 -15 -14   9
+G  -2  -3  -9  -3  -4  -9   6
+H  -7  -1  -7  -4  -5  -6  -9   9
+I  -5  -6  -6  -7  -5  -2 -11  -9   8
+K  -7  -2 -14  -4  -4 -14  -7  -6  -6   7
+L  -6  -9 -15 -12  -9  -3 -10  -6  -1  -8   7
+M  -5 -10 -13 -11  -7  -4  -8 -10  -1  -2   1  11
+N  -4   6 -11   2  -2  -9  -3   0  -5  -1  -7  -9   8
+P  -2  -7  -8  -8  -5 -10  -6  -4  -8  -6  -7  -8  -6   8
+Q  -4  -3 -14  -2   1 -13  -7   1  -8  -3  -5  -4  -3  -3   8
+R  -7  -7  -8 -10  -9  -9  -9  -2  -5   0  -8  -4  -6  -4  -2   8
+S   0  -1  -3  -4  -4  -6  -2  -6  -7  -4  -8  -5   0  -2  -5  -3   6
+T  -1  -3  -8  -5  -6  -9  -6  -7  -2  -3  -7  -4  -2  -4  -5  -6   0   7
+V  -2  -8  -6  -8  -6  -8  -5  -6   2  -9  -2  -1  -8  -6  -7  -8  -6  -3   7
+W -13 -10 -15 -15 -17  -4 -15  -7 -14 -12  -6 -13  -8 -14 -13  -2  -5 -13 -15  13
+X  -3  -5  -9  -5  -5  -8  -5  -5  -5  -5  -6  -5  -3  -5  -5  -6  -3  -4  -5 -11  -5
+Y  -8  -6  -4 -11  -8   2 -14  -3  -6  -9  -7 -11  -4 -13 -12 -10  -7  -6  -7  -5  -7  10
+Z  -3   0 -14   1   6 -13  -5  -1  -6  -4  -7  -5  -3  -4   6  -4  -5  -6  -6 -14  -5  -9   6
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam300
+------------
+A   2
+B   0   3
+C  -2  -5  15
+D   0   3  -6   4
+E   0   3  -6   4   4
+F  -4  -5  -5  -6  -6  11
+G   2   1  -4   1   0  -5   5
+H  -1   1  -4   1   1  -2  -2   7
+I   0  -2  -3  -2  -2   1  -3  -2   5
+K  -1   1  -6   0   0  -6  -2   0  -2   5
+L  -2  -4  -7  -4  -4   3  -4  -2   3  -3   7
+M  -1  -2  -6  -3  -2   1  -3  -2   3   0   4   6
+N   0   2  -4   2   2  -4   1   2  -2   1  -3  -2   2
+P   1   0  -3  -1   0  -5   0   0  -2  -1  -3  -2   0   6
+Q   0   2  -6   2   3  -5  -1   3  -2   1  -2  -1   1   0   4
+R  -1   0  -4  -1  -1  -5  -2   2  -2   4  -3   0   0   0   2   7
+S   1   1   0   0   0  -4   1  -1  -1   0  -3  -2   1   1   0   0   1
+T   1   0  -2   0   0  -3   0  -1   0   0  -2  -1   0   1  -1  -1   1   2
+V   0  -2  -2  -2  -2  -1  -1  -2   4  -2   2   2  -2  -1  -2  -3  -1   0   5
+W  -6  -6  -9  -7  -8   1  -8  -3  -6  -4  -2  -5  -5  -6  -5   3  -3  -6  -7  22
+X   0   0  -3  -1  -1  -2  -1   0  -1  -1  -1  -1   0  -1   0  -1   0   0   0  -4  -1
+Y  -4  -4   1  -5  -5   9  -6   0  -1  -5   0  -2  -2  -5  -4  -5  -3  -3  -3   0  -2  12
+Z   0   2  -6   3   3  -5   0   2  -2   1  -3  -2   1   0   3   0   0   0  -2  -6  -1  -5   3
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam60
+------------
+A   5
+B  -2   5
+C  -5  -9   9
+D  -2   5 -10   7
+E  -1   2 -10   3   7
+F  -6  -8  -9 -11 -10   8
+G   0  -2  -7  -2  -2  -7   6
+H  -5   0  -6  -2  -3  -4  -6   8
+I  -3  -4  -4  -5  -4  -1  -7  -6   7
+K  -5  -1 -10  -2  -3 -10  -5  -4  -4   6
+L  -4  -7 -11  -9  -7  -1  -8  -4   0  -6   6
+M  -3  -6 -10  -7  -5  -2  -6  -7   1   0   2  10
+N  -2   5  -7   2   0  -6  -1   1  -4   0  -5  -6   6
+P   0  -4  -6  -5  -3  -7  -4  -2  -6  -4  -5  -6  -4   7
+Q  -3  -1 -10  -1   2  -9  -5   2  -5  -1  -3  -2  -2  -1   7
+R  -5  -5  -6  -6  -6  -7  -7   0  -4   2  -6  -2  -3  -2   0   8
+S   1   0  -1  -2  -2  -5   0  -4  -4  -2  -6  -4   1   0  -3  -2   5
+T   1  -2  -5  -3  -4  -6  -3  -5  -1  -2  -5  -2  -1  -2  -4  -4   1   6
+V  -1  -5  -4  -6  -4  -5  -4  -5   3  -6  -1   0  -5  -4  -5  -5  -4  -1   6
+W -10  -8 -12 -11 -12  -3 -11  -5 -10  -8  -4  -9  -6 -10  -9   0  -4  -9 -11  13
+X  -2  -3  -6  -3  -3  -5  -3  -3  -3  -3  -4  -3  -2  -3  -3  -4  -2  -2  -3  -8  -3
+Y  -6  -5  -2  -8  -7   3 -10  -2  -4  -7  -5  -7  -3 -10  -8  -8  -5  -5  -5  -3  -5   9
+Z  -2   1 -10   2   5 -10  -3   0  -4  -2  -5  -4  -1  -2   6  -2  -3  -4  -5 -11  -3  -7   5
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   X   Y   Z
+
+pam90
+------------
+A   4
+B  -1   4
+C  -3  -7   9
+D  -1   5  -8   6
+E   0   2  -8   4   6
+F  -5  -6  -7  -8  -8   8
+G   0  -1  -5  -1  -1  -6   5
+H  -4   1  -5  -1  -1  -3  -5   8
+I  -2  -3  -3  -4  -3   0  -5  -5   6
+K  -3   0  -8  -2  -2  -8  -4  -2  -3   5
+L  -3  -5  -9  -7  -5   0  -6  -3   1  -5   6
+M  -2  -5  -8  -5  -4  -1  -5  -5   1   0   2   9
+N  -1   4  -6   3   0  -5  -1   2  -3   1  -4  -4   5
+P   0  -3  -5  -4  -2  -6  -3  -2  -4  -3  -4  -4  -2   7
+Q  -2   0  -8   0   2  -7  -3   2  -4  -1  -3  -2  -1  -1   6
+R  -4  -3  -5  -5  -4  -6  -5   1  -3   2  -5  -2  -2  -1   0   7
+S   1   0  -1  -1  -2  -4   0  -3  -3  -1  -5  -3   1   0  -2  -1   4
+T   1  -1  -4  -2  -2  -5  -2  -3   0  -1  -3  -2   0  -1  -3  -3   2   5
+V   0  -4  -3  -4  -3  -4  -3  -4   3  -5   0   1  -4  -3  -4  -4  -3  -1   6
+W  -8  -7 -10  -9 -10  -2  -9  -4  -8  -6  -3  -7  -5  -8  -7   0  -3  -7  -9  13
+Y  -5  -4  -1  -6  -6   4  -8  -1  -3  -6  -3  -6  -2  -8  -6  -6  -4  -4  -4  -2   9
+Z  -1   2  -8   3   5  -8  -2   1  -3  -1  -4  -3   0  -2   5  -1  -2  -2  -3  -8  -6   5
+   A   B   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y   Z
+
+rao
+------------
+A  16
+C  11  16
+D   9   8  16
+E  10   9  11  16
+F  10  10   4   6  16
+G   8   8   9   6   7  16
+H  11  10   9  11   9   7  16
+I   9   8   3   4  12   6   8  16
+K  10   9  11  11   6   7  11   4  16
+L  11  11   6   7  11   6  10  10   7  16
+M  11  10   5   8  10   4  10   9   8  11  16
+N   9   9  11  10   6  10  10   5  11   7   6  16
+P   6   7   8   5   4  11   5   3   6   4   2   9  16
+Q  11  10  11  11   7   8  11   6  12   9   9  11   7  16
+R   8   8  10   9   5   7  10   4  11   6   6  10   6  10  16
+S  10  10  10   9   8  11  10   8  10   8   7  11  10  10   9  16
+T  10  10   9   8  10  10  10  10   9   9   8  10   8  10   9  11  16
+V   9   8   3   4  11   6   9  12   5  10   9   5   3   6   5   8  10  16
+W  11  11   6   7  11   8  10  11   7  11  10   8   6   9   7  10  11  11  16
+Y   9  10   7   6  10  10   9  10   7   9   8   8   8   8   7  11  11  10  11  16
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+risler
+------------
+A   2
+C  -1   2
+D   0  -1   2
+E   1  -1   1   2
+F   0  -1   0   0   2
+G   0  -1   0   0   0   2
+H   0  -1  -1   0  -1  -1   2
+I   1  -1   0   1   1   0   0   2
+K   1  -1   0   1   0   0  -1   1   2
+L   1  -1   0   0   1   0   0   2   0   2
+M   1  -1   0   0   0   0  -1   0   0   1   2
+N   1  -1   0   1   0   0   0   0   1   0   0   2
+P   0  -1  -1   0  -1  -1  -1   0   0   0  -1  -1   2
+Q   1  -1   0   2   0   0   0   1   1   1   1   1   0   2
+R   1  -1   0   1   0   0   0   1   2   1   1   1   0   2   2
+S   2  -1   0   1   0   0   0   1   1   1   0   1   0   1   2   2
+T   1  -1   0   1   0   0   0   1   1   1   0   1   0   1   1   2   2
+V   2  -1   0   1   0   0   0   2   1   2   0   1   0   1   1   1   1   2
+W   0  -1  -1  -1   0  -1  -1   0  -1   0  -1  -1  -1  -1   0   0  -1   0   2
+Y   0  -1   0   0   2   0   0   0   0   0   0   0  -1   0   0   0   0   0   0   2
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
+
+str
+------------
+A   4
+C  -2  11
+D  -1  -7   6
+E   0  -3   2   5
+F  -3  -2  -5  -4   7
+G   0  -6  -1  -2  -6   5
+H  -2  -6   0  -2  -2  -3   8
+I  -2  -4  -3  -3   1  -5  -5   6
+K  -1  -4  -1   1  -3  -3   0  -3   5
+L  -2  -6  -6  -4   2  -5  -3   2  -2   5
+M   0  -5  -4  -2   0  -4  -2   1  -1   3   8
+N  -1  -6   2   0  -3  -1   2  -3   0  -3  -2   5
+P  -1  -8  -1  -1  -5  -2  -3  -4  -1  -3  -6  -2   7
+Q   0  -3   0   2  -4  -2   0  -5   1  -3   1   0  -2   6
+R  -1  -2  -2   0  -4  -2   0  -3   2  -3  -4  -1  -2   1   7
+S   0  -4   0  -1  -3  -1  -2  -3  -1  -4  -4   0  -1  -1   0   4
+T  -1  -5  -1   0  -3  -3  -2  -2   0  -3  -2   0  -1   0  -1   1   5
+V   0  -4  -4  -2  -1  -4  -2   2  -3   1   0  -4  -4  -2  -3  -3  -1   5
+W  -3  -6  -6  -6   2  -4  -3  -2  -3  -1  -2  -5  -4  -5  -2  -5  -5  -4  10
+Y  -3  -6  -3  -2   3  -3   0  -1  -2  -2  -1  -1  -6  -3  -1  -2  -2  -1   2   7
+   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y
diff --git a/Tests/test_SubsMat.py b/Tests/test_SubsMat.py
new file mode 100644
index 00000000000..655825aa8ef
--- /dev/null
+++ b/Tests/test_SubsMat.py
@@ -0,0 +1,40 @@
+import cPickle
+import sys
+from Bio.SubsMat import *
+
+f = sys.stdout
+ftab_prot = FreqTable.read_count(open('SubsMat/protein_count.txt'))
+ctab_prot = FreqTable.read_freq(open('SubsMat/protein_freq.txt'))
+f.write("Check differences between derived and true frequencies for each\n")
+f.write("letter. Differences should be very small\n")
+for i in ftab_prot.alphabet.letters:
+    f.write("%s %f\n" % (i, abs(ftab_prot[i] - ctab_prot[i])))
+    
+acc_rep_mat = cPickle.load(open('SubsMat/acc_rep_mat.pik'))
+acc_rep_mat = SubsMat.SeqMat(acc_rep_mat)
+obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)
+ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)
+obs_freq_mat.print_mat(f=f,format=" %4.3f")
+
+
+f.write("Diff between supplied and matrix-derived frequencies, should be small\n")
+for i in ftab_prot.keys():
+    f.write("%s %.2f\n" % (i,abs(ftab_prot[i] - ftab_prot2[i])))
+
+s = 0.
+f.write("Calculating sum of letters for an observed frequency matrix\n")
+obs_freq_mat.all_letters_sum()
+for i in obs_freq_mat.sum_letters.keys():
+    f.write("%s\t%.2f\n" % (i, obs_freq_mat.sum_letters[i]))
+    s += obs_freq_mat.sum_letters[i]
+f.write("Total sum %.2f should be 1.0\n" % (s))
+lo_mat_prot = \
+SubsMat.make_log_odds_matrix(acc_rep_mat=acc_rep_mat,round_digit=1) #,ftab_prot
+f.write("\nLog odds matrix\n")
+lo_mat_prot.print_mat(f=f,format=" %.2f",alphabet='AVILMCFWYHSTNQKRDEGP')
+
+f.write("\nTesting MatrixInfo\n")
+for i in MatrixInfo.available_matrices:
+    mat = SubsMat.SeqMat(getattr(MatrixInfo,i))
+    f.write("\n%s\n------------\n" % i)
+    mat.print_mat(f=f)
diff --git a/Tests/test_align.py b/Tests/test_align.py
index 6ec763a9b9b..ef465302786 100644
--- a/Tests/test_align.py
+++ b/Tests/test_align.py
@@ -12,10 +12,12 @@
 import os 
 
 # biopython
+from Bio.Alphabet import IUPAC
 from Bio.Clustalw import Clustalw
 from Bio.Align.FormatConvert import FormatConverter
 from Bio.Align import AlignInfo
 from Bio.Fasta import FastaAlign
+from Bio.SubsMat import FreqTable
 
 print "testing reading and writing clustal format..."
 test_dir = os.path.join(os.getcwd(), 'Clustalw')
@@ -74,8 +76,11 @@
           'A' : 0.25,
           'T' : 0.25}
 
+e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
+                                   IUPAC.unambiguous_dna)
+
 print 'relative information:', align_info.information_content(
-                                   expected_freqs = e_freq,
+                                   e_freq_table = e_freq_table,
                                    chars_to_ignore = ['N'])
 
 print "testing reading and writing fasta format..."