stride-align 0.6.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (190) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE +201 -0
  3. data/NOTICE +255 -0
  4. data/README.md +107 -0
  5. data/data/bmpm_data/gen_approx_any.txt +131 -0
  6. data/data/bmpm_data/gen_approx_arabic.txt +26 -0
  7. data/data/bmpm_data/gen_approx_common.txt +233 -0
  8. data/data/bmpm_data/gen_approx_cyrillic.txt +18 -0
  9. data/data/bmpm_data/gen_approx_czech.txt +18 -0
  10. data/data/bmpm_data/gen_approx_dutch.txt +18 -0
  11. data/data/bmpm_data/gen_approx_english.txt +47 -0
  12. data/data/bmpm_data/gen_approx_french.txt +25 -0
  13. data/data/bmpm_data/gen_approx_german.txt +73 -0
  14. data/data/bmpm_data/gen_approx_greek.txt +18 -0
  15. data/data/bmpm_data/gen_approx_greeklatin.txt +20 -0
  16. data/data/bmpm_data/gen_approx_hebrew.txt +18 -0
  17. data/data/bmpm_data/gen_approx_hungarian.txt +18 -0
  18. data/data/bmpm_data/gen_approx_italian.txt +18 -0
  19. data/data/bmpm_data/gen_approx_polish.txt +84 -0
  20. data/data/bmpm_data/gen_approx_portuguese.txt +18 -0
  21. data/data/bmpm_data/gen_approx_romanian.txt +18 -0
  22. data/data/bmpm_data/gen_approx_russian.txt +48 -0
  23. data/data/bmpm_data/gen_approx_spanish.txt +21 -0
  24. data/data/bmpm_data/gen_approx_turkish.txt +18 -0
  25. data/data/bmpm_data/gen_exact_any.txt +40 -0
  26. data/data/bmpm_data/gen_exact_approx_common.txt +79 -0
  27. data/data/bmpm_data/gen_exact_arabic.txt +18 -0
  28. data/data/bmpm_data/gen_exact_common.txt +32 -0
  29. data/data/bmpm_data/gen_exact_cyrillic.txt +18 -0
  30. data/data/bmpm_data/gen_exact_czech.txt +18 -0
  31. data/data/bmpm_data/gen_exact_dutch.txt +18 -0
  32. data/data/bmpm_data/gen_exact_english.txt +18 -0
  33. data/data/bmpm_data/gen_exact_french.txt +18 -0
  34. data/data/bmpm_data/gen_exact_german.txt +18 -0
  35. data/data/bmpm_data/gen_exact_greek.txt +18 -0
  36. data/data/bmpm_data/gen_exact_greeklatin.txt +18 -0
  37. data/data/bmpm_data/gen_exact_hebrew.txt +18 -0
  38. data/data/bmpm_data/gen_exact_hungarian.txt +18 -0
  39. data/data/bmpm_data/gen_exact_italian.txt +18 -0
  40. data/data/bmpm_data/gen_exact_polish.txt +23 -0
  41. data/data/bmpm_data/gen_exact_portuguese.txt +18 -0
  42. data/data/bmpm_data/gen_exact_romanian.txt +18 -0
  43. data/data/bmpm_data/gen_exact_russian.txt +19 -0
  44. data/data/bmpm_data/gen_exact_spanish.txt +19 -0
  45. data/data/bmpm_data/gen_exact_turkish.txt +18 -0
  46. data/data/bmpm_data/gen_hebrew_common.txt +113 -0
  47. data/data/bmpm_data/gen_lang.txt +295 -0
  48. data/data/bmpm_data/gen_languages.txt +36 -0
  49. data/data/bmpm_data/gen_rules_any.txt +367 -0
  50. data/data/bmpm_data/gen_rules_arabic.txt +76 -0
  51. data/data/bmpm_data/gen_rules_cyrillic.txt +99 -0
  52. data/data/bmpm_data/gen_rules_czech.txt +67 -0
  53. data/data/bmpm_data/gen_rules_dutch.txt +78 -0
  54. data/data/bmpm_data/gen_rules_english.txt +113 -0
  55. data/data/bmpm_data/gen_rules_french.txt +114 -0
  56. data/data/bmpm_data/gen_rules_german.txt +129 -0
  57. data/data/bmpm_data/gen_rules_greek.txt +97 -0
  58. data/data/bmpm_data/gen_rules_greeklatin.txt +118 -0
  59. data/data/bmpm_data/gen_rules_hebrew.txt +62 -0
  60. data/data/bmpm_data/gen_rules_hungarian.txt +83 -0
  61. data/data/bmpm_data/gen_rules_italian.txt +77 -0
  62. data/data/bmpm_data/gen_rules_polish.txt +185 -0
  63. data/data/bmpm_data/gen_rules_portuguese.txt +105 -0
  64. data/data/bmpm_data/gen_rules_romanian.txt +64 -0
  65. data/data/bmpm_data/gen_rules_russian.txt +142 -0
  66. data/data/bmpm_data/gen_rules_spanish.txt +85 -0
  67. data/data/bmpm_data/gen_rules_turkish.txt +50 -0
  68. data/data/keyboard_data/qwerty.npy +0 -0
  69. data/data/matrix_data/BLOSUM100 +31 -0
  70. data/data/matrix_data/BLOSUM30 +31 -0
  71. data/data/matrix_data/BLOSUM35 +31 -0
  72. data/data/matrix_data/BLOSUM40 +31 -0
  73. data/data/matrix_data/BLOSUM45 +25 -0
  74. data/data/matrix_data/BLOSUM50 +25 -0
  75. data/data/matrix_data/BLOSUM55 +31 -0
  76. data/data/matrix_data/BLOSUM60 +31 -0
  77. data/data/matrix_data/BLOSUM62 +25 -0
  78. data/data/matrix_data/BLOSUM65 +31 -0
  79. data/data/matrix_data/BLOSUM70 +31 -0
  80. data/data/matrix_data/BLOSUM75 +31 -0
  81. data/data/matrix_data/BLOSUM80 +25 -0
  82. data/data/matrix_data/BLOSUM85 +31 -0
  83. data/data/matrix_data/BLOSUM90 +25 -0
  84. data/data/matrix_data/NUC.4.4 +25 -0
  85. data/data/matrix_data/PAM10 +34 -0
  86. data/data/matrix_data/PAM100 +34 -0
  87. data/data/matrix_data/PAM110 +34 -0
  88. data/data/matrix_data/PAM120 +34 -0
  89. data/data/matrix_data/PAM130 +34 -0
  90. data/data/matrix_data/PAM140 +34 -0
  91. data/data/matrix_data/PAM150 +34 -0
  92. data/data/matrix_data/PAM160 +34 -0
  93. data/data/matrix_data/PAM170 +34 -0
  94. data/data/matrix_data/PAM180 +34 -0
  95. data/data/matrix_data/PAM190 +34 -0
  96. data/data/matrix_data/PAM20 +34 -0
  97. data/data/matrix_data/PAM200 +34 -0
  98. data/data/matrix_data/PAM210 +34 -0
  99. data/data/matrix_data/PAM220 +34 -0
  100. data/data/matrix_data/PAM230 +34 -0
  101. data/data/matrix_data/PAM240 +34 -0
  102. data/data/matrix_data/PAM250 +25 -0
  103. data/data/matrix_data/PAM260 +34 -0
  104. data/data/matrix_data/PAM270 +34 -0
  105. data/data/matrix_data/PAM280 +34 -0
  106. data/data/matrix_data/PAM290 +34 -0
  107. data/data/matrix_data/PAM30 +25 -0
  108. data/data/matrix_data/PAM300 +34 -0
  109. data/data/matrix_data/PAM310 +34 -0
  110. data/data/matrix_data/PAM320 +34 -0
  111. data/data/matrix_data/PAM330 +34 -0
  112. data/data/matrix_data/PAM340 +34 -0
  113. data/data/matrix_data/PAM350 +34 -0
  114. data/data/matrix_data/PAM360 +34 -0
  115. data/data/matrix_data/PAM370 +34 -0
  116. data/data/matrix_data/PAM380 +34 -0
  117. data/data/matrix_data/PAM390 +34 -0
  118. data/data/matrix_data/PAM40 +34 -0
  119. data/data/matrix_data/PAM400 +34 -0
  120. data/data/matrix_data/PAM410 +34 -0
  121. data/data/matrix_data/PAM420 +34 -0
  122. data/data/matrix_data/PAM430 +34 -0
  123. data/data/matrix_data/PAM440 +34 -0
  124. data/data/matrix_data/PAM450 +34 -0
  125. data/data/matrix_data/PAM460 +34 -0
  126. data/data/matrix_data/PAM470 +34 -0
  127. data/data/matrix_data/PAM480 +34 -0
  128. data/data/matrix_data/PAM490 +34 -0
  129. data/data/matrix_data/PAM50 +34 -0
  130. data/data/matrix_data/PAM500 +34 -0
  131. data/data/matrix_data/PAM60 +34 -0
  132. data/data/matrix_data/PAM70 +25 -0
  133. data/data/matrix_data/PAM80 +34 -0
  134. data/data/matrix_data/PAM90 +34 -0
  135. data/ext/stride_align/backend_avx2.cpp +2 -0
  136. data/ext/stride_align/backend_avx512bwvl.cpp +2 -0
  137. data/ext/stride_align/backend_generic.cpp +3 -0
  138. data/ext/stride_align/backend_impl.hpp +983 -0
  139. data/ext/stride_align/backend_lasx.cpp +2 -0
  140. data/ext/stride_align/backend_lsx.cpp +2 -0
  141. data/ext/stride_align/backend_neon.cpp +2 -0
  142. data/ext/stride_align/backend_rvv.cpp +2 -0
  143. data/ext/stride_align/backend_sse41.cpp +2 -0
  144. data/ext/stride_align/backend_sve.cpp +2 -0
  145. data/ext/stride_align/backend_sve2.cpp +2 -0
  146. data/ext/stride_align/backend_vsx.cpp +2 -0
  147. data/ext/stride_align/beider_morse_impl.cpp +5 -0
  148. data/ext/stride_align/cpu_detect.cpp +172 -0
  149. data/ext/stride_align/cpu_detect.hpp +6 -0
  150. data/ext/stride_align/extconf.rb +114 -0
  151. data/ext/stride_align/target_profile.hpp +82 -0
  152. data/ext/stride_align/vendor/beider_morse_impl.cpp +1467 -0
  153. data/ext/stride_align/vendor/stride_align/alignment.hpp +199 -0
  154. data/ext/stride_align/vendor/stride_align/batch.hpp +812 -0
  155. data/ext/stride_align/vendor/stride_align/beider_morse.hpp +121 -0
  156. data/ext/stride_align/vendor/stride_align/caverphone.hpp +222 -0
  157. data/ext/stride_align/vendor/stride_align/cologne_phonetic.hpp +202 -0
  158. data/ext/stride_align/vendor/stride_align/core.hpp +731 -0
  159. data/ext/stride_align/vendor/stride_align/daitch_mokotoff.hpp +631 -0
  160. data/ext/stride_align/vendor/stride_align/double_metaphone.hpp +796 -0
  161. data/ext/stride_align/vendor/stride_align/dtw.hpp +300 -0
  162. data/ext/stride_align/vendor/stride_align/encoded.hpp +235 -0
  163. data/ext/stride_align/vendor/stride_align/hamming.hpp +55 -0
  164. data/ext/stride_align/vendor/stride_align/indel.hpp +1200 -0
  165. data/ext/stride_align/vendor/stride_align/jaro.hpp +517 -0
  166. data/ext/stride_align/vendor/stride_align/lcs.hpp +159 -0
  167. data/ext/stride_align/vendor/stride_align/levenshtein.hpp +1247 -0
  168. data/ext/stride_align/vendor/stride_align/levenshtein_prepared.hpp +193 -0
  169. data/ext/stride_align/vendor/stride_align/match_rating.hpp +168 -0
  170. data/ext/stride_align/vendor/stride_align/metaphone.hpp +291 -0
  171. data/ext/stride_align/vendor/stride_align/ngram.hpp +176 -0
  172. data/ext/stride_align/vendor/stride_align/nysiis.hpp +199 -0
  173. data/ext/stride_align/vendor/stride_align/pairwise_alignment.hpp +465 -0
  174. data/ext/stride_align/vendor/stride_align/partial_ratio.hpp +486 -0
  175. data/ext/stride_align/vendor/stride_align/ratcliff_obershelp.hpp +101 -0
  176. data/ext/stride_align/vendor/stride_align/soundex.hpp +108 -0
  177. data/ext/stride_align/vendor/stride_align/token_ratios.hpp +445 -0
  178. data/ext/stride_align/vendor/stride_align/types.hpp +16 -0
  179. data/ext/stride_align/vendor/stride_align/utf8.hpp +512 -0
  180. data/ext/stride_align/vendor/stride_align/wratio.hpp +363 -0
  181. data/lib/stride_align/algorithms.rb +296 -0
  182. data/lib/stride_align/alignment_path.rb +217 -0
  183. data/lib/stride_align/backend.rb +47 -0
  184. data/lib/stride_align/batch.rb +705 -0
  185. data/lib/stride_align/core.rb +180 -0
  186. data/lib/stride_align/keyboard.rb +200 -0
  187. data/lib/stride_align/matrices.rb +403 -0
  188. data/lib/stride_align/version.rb +5 -0
  189. data/lib/stride_align.rb +87 -0
  190. metadata +231 -0
data/data/matrix_data/PAM210 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049
5
+ #
6
+ # Expected score = -1.12, Entropy = 0.470 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 18
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
12
+ R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9
13
+ N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
14
+ D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9
15
+ C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9
16
+ Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9
17
+ E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9
18
+ G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9
19
+ H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9
20
+ I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9
21
+ L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9
22
+ K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9
23
+ M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
24
+ F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9
25
+ P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9
26
+ S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9
27
+ T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9
28
+ W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9
29
+ Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9
31
+ B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
32
+ Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9
33
+ X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM220 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049
5
+ #
6
+ # Expected score = -1.06, Entropy = 0.437 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 17
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
12
+ R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
13
+ N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
14
+ D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8
15
+ C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8
16
+ Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8
17
+ E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
18
+ G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8
19
+ H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8
20
+ I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
21
+ L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
22
+ K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8
23
+ M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8
24
+ F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8
25
+ P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8
26
+ S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8
27
+ T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8
28
+ W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8
29
+ Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8
31
+ B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
32
+ Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8
33
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM230 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049
5
+ #
6
+ # Expected score = -0.991, Entropy = 0.407 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 17
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
12
+ R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
13
+ N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
14
+ D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8
15
+ C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
16
+ Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8
17
+ E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
18
+ G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8
19
+ H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8
20
+ I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
21
+ L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
22
+ K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8
23
+ M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8
24
+ F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8
25
+ P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
26
+ S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8
27
+ T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8
28
+ W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8
29
+ Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8
30
+ V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8
31
+ B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
32
+ Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8
33
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM240 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049
5
+ #
6
+ # Expected score = -0.923, Entropy = 0.379 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 17
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
12
+ R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8
13
+ N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
14
+ D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
15
+ C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
16
+ Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
17
+ E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
18
+ G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
19
+ H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
20
+ I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8
22
+ K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8
23
+ M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8
24
+ F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8
25
+ P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
26
+ S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8
27
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
28
+ W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8
29
+ Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8
30
+ V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8
31
+ B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8
32
+ Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
33
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM250 ADDED
@@ -0,0 +1,25 @@
1
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
2
+ A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
3
+ R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
4
+ N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8
5
+ D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
6
+ C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
7
+ Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
8
+ E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
9
+ G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8
10
+ H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
11
+ I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
12
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
13
+ K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
14
+ M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
15
+ F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
16
+ P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
17
+ S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
18
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
19
+ W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
20
+ Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
21
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
22
+ B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
23
+ Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
24
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
25
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM260 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049
5
+ #
6
+ # Expected score = -0.794, Entropy = 0.330 bits
7
+ #
8
+ # Lowest score = -7, Highest score = 17
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7
12
+ R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7
13
+ N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7
14
+ D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7
15
+ C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7
16
+ Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7
17
+ E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7
18
+ G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7
19
+ H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7
22
+ K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7
23
+ M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7
24
+ F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7
25
+ P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7
27
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7
28
+ W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7
29
+ Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7
30
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7
31
+ B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7
32
+ Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7
33
+ X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7
34
+ * -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
data/data/matrix_data/PAM270 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.969, Entropy = 0.309 bits
7
+ #
8
+ # Lowest score = -10, Highest score = 23
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10
12
+ R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
14
+ D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10
15
+ C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10
16
+ Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10
17
+ E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10
18
+ G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10
19
+ H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10
20
+ I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10
21
+ L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10
22
+ K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10
23
+ M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10
24
+ F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10
25
+ P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10
26
+ S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10
27
+ T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10
28
+ W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10
29
+ Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10
30
+ V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10
31
+ B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10
32
+ Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10
33
+ X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10
34
+ * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
data/data/matrix_data/PAM280 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.916, Entropy = 0.289 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
12
+ R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
14
+ D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9
15
+ C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9
17
+ E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
18
+ G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9
20
+ I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9
21
+ L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
22
+ K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
23
+ M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9
24
+ F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9
25
+ P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9
26
+ S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
27
+ T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9
28
+ W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9
29
+ Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9
30
+ V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
31
+ B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
32
+ Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
33
+ X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM290 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.877, Entropy = 0.271 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
12
+ R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
14
+ D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9
15
+ C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9
17
+ E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
18
+ G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9
20
+ I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
21
+ L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
22
+ K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
23
+ M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
24
+ F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9
25
+ P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
27
+ T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9
28
+ W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9
29
+ Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9
30
+ V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
31
+ B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9
32
+ Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
33
+ X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM30 ADDED
@@ -0,0 +1,25 @@
1
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
2
+ A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
3
+ R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
4
+ N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
5
+ D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
6
+ C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
7
+ Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
8
+ E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
9
+ G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
10
+ H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
11
+ I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
12
+ L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
13
+ K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
14
+ M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
15
+ F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
16
+ P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
17
+ S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
18
+ T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
19
+ W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
20
+ Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
21
+ V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
22
+ B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
23
+ Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
24
+ X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
25
+ * -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
data/data/matrix_data/PAM300 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.835, Entropy = 0.254 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
12
+ R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9
14
+ D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
15
+ C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
17
+ E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9
18
+ G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
20
+ I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
21
+ L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9
22
+ K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
23
+ M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
24
+ F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
25
+ P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
27
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
28
+ W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
29
+ Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9
30
+ V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9
31
+ B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
32
+ Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9
33
+ X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM310 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.779, Entropy = 0.238 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
12
+ R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9
14
+ D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
15
+ C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
17
+ E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9
18
+ G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9
22
+ K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9
23
+ M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9
24
+ F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
25
+ P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
27
+ T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
28
+ W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
29
+ Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9
30
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
31
+ B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
32
+ Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9
33
+ X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM320 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.741, Entropy = 0.224 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
12
+ R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8
13
+ N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8
14
+ D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8
15
+ C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
16
+ Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8
17
+ E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8
18
+ G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8
19
+ H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8
22
+ K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8
23
+ M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8
24
+ F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8
25
+ P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
27
+ T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8
28
+ W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8
29
+ Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
30
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
31
+ B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8
32
+ Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8
33
+ X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM330 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.693, Entropy = 0.210 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
12
+ R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8
13
+ N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
14
+ D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
15
+ C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
16
+ Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
17
+ E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8
18
+ G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
19
+ H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8
22
+ K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8
23
+ M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
24
+ F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8
25
+ P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
26
+ S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
27
+ T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
28
+ W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8
29
+ Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
30
+ V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
31
+ B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
32
+ Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
33
+ X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM340 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287
5
+ #
6
+ # Expected score = -0.680, Entropy = 0.198 bits
7
+ #
8
+ # Lowest score = -8, Highest score = 22
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
12
+ R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8
13
+ N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
14
+ D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
15
+ C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
16
+ Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
17
+ E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
18
+ G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
19
+ H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8
22
+ K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8
23
+ M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
24
+ F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8
25
+ P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8
26
+ S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
27
+ T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
28
+ W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8
29
+ Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
30
+ V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
31
+ B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
32
+ Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
33
+ X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
34
+ * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
data/data/matrix_data/PAM350 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629
5
+ #
6
+ # Expected score = -0.701, Entropy = 0.186 bits
7
+ #
8
+ # Lowest score = -10, Highest score = 27
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
12
+ R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10
13
+ N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
14
+ D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10
15
+ C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10
16
+ Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10
17
+ E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10
18
+ G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10
19
+ H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10
20
+ I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
21
+ L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10
22
+ K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10
23
+ M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10
24
+ F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10
25
+ P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10
26
+ S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10
27
+ T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10
28
+ W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10
29
+ Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10
30
+ V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10
31
+ B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10
32
+ Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10
33
+ X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10
34
+ * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
data/data/matrix_data/PAM360 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629
5
+ #
6
+ # Expected score = -0.697, Entropy = 0.175 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 27
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
12
+ R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9
13
+ N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9
14
+ D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9
15
+ C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
17
+ E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
18
+ G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
20
+ I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9
21
+ L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9
22
+ K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
23
+ M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9
24
+ F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9
25
+ P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
26
+ S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
27
+ T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
28
+ W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9
29
+ Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
30
+ V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
31
+ B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
32
+ Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9
33
+ X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
data/data/matrix_data/PAM370 ADDED
@@ -0,0 +1,34 @@
1
+ #
2
+ # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
3
+ #
4
+ # PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629
5
+ #
6
+ # Expected score = -0.649, Entropy = 0.165 bits
7
+ #
8
+ # Lowest score = -9, Highest score = 27
9
+ #
10
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
11
+ A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
12
+ R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9
13
+ N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9
14
+ D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
15
+ C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
16
+ Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
17
+ E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
18
+ G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9
19
+ H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
20
+ I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
21
+ L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9
22
+ K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9
23
+ M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9
24
+ F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9
25
+ P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
26
+ S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
27
+ T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
28
+ W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9
29
+ Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
30
+ V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9
31
+ B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
32
+ Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9
33
+ X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
34
+ * -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1