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"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 17:10:43 +0000
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-1:000000000000 0:b15a3147e604
1 /* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
2 ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
3
4 trimAl v1.4: a tool for automated alignment trimming in large-scale
5 phylogenetics analyses.
6
7 2009-2015 Capella-Gutierrez S. and Gabaldon, T.
8 [scapella, tgabaldon]@crg.es
9
10 This file is part of trimAl.
11
12 trimAl is free software: you can redistribute it and/or modify
13 it under the terms of the GNU General Public License as published by
14 the Free Software Foundation, the last available version.
15
16 trimAl is distributed in the hope that it will be useful,
17 but WITHOUT ANY WARRANTY; without even the implied warranty of
18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 GNU General Public License for more details.
20
21 You should have received a copy of the GNU General Public License
22 along with trimAl. If not, see <http://www.gnu.org/licenses/>.
23
24 ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** *****
25 ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */
26
27 #ifdef SIMMatrix
28
29 /* Characters used for different alignments type */
30 char listNTSym[6] = "ACGTU";
31
32 char listAASym[21] = "ARNDCQEGHILKMFPSTWYV";
33
34 char listNTDegenerateSym[16] = "ACGTURYKMSWBDHV";
35
36 /* Characters used to indicate indeterminations */
37 char protein_wildcards[3] = "BX";
38
39 /* Pyrrolysine: 'O' > 'TAG' */
40 /* Selenocysteine: 'U' > 'TGA' */
41 char protein_alternative_aminoacids[3] = "UO";
42
43 /* Default Identity Matrix for Canonical Nucleotides */
44 float defaultNTMatrix[5][5] = {
45 {1, 0, 0, 0, 0},
46 {0, 1, 0, 0, 0},
47 {0, 0, 1, 0, 0},
48 {0, 0, 0, 1, 0},
49 {0, 0, 0, 0, 1}
50 };
51
52 float defaultNTDegeneratedMatrix[15][15] = {
53 /* A: adenosine (A) C: cytidine (C) G: guanine (G) T: thymidine (T) U: uridine (U)
54 * R: purine (G | A) Y: pyrimidine (C | T/u) K: keto (G | T/u) M: amino (A | C) S: strong (G | C)
55 * W: weak (A | T/u) B: not A (G | C | T/u) D: not C (G | A | T/u) H: not G (A | C | T/u) V: not T/u (G | C | A) */
56 { 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
57 { 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
58 { 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
59 { 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
60 { 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
61 { 1/4., 0.0, 1/4., 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
62 { 0.0, 1/4., 0.0, 1/4., 1/4., 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
63 { 0.0, 0.0, 1/4., 1/4., 1/4., 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
64 { 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
65 { 0.0, 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0, 0.0},
66 { 1/4., 0.0, 0.0, 1/4., 1/4., 0.0, 0.0, 0.0, 0.0, 0.0, 1/4., 0.0, 0.0, 0.0, 0.0},
67 { 0.0, 1/6., 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0, 0.0, 0.0},
68 { 1/6., 0.0, 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0, 0.0},
69 { 1/6., 1/6., 0.0, 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6., 0.0},
70 { 1/6., 1/6., 1/6., 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1/6.}
71 };
72
73 /* BLOSUM62 Similarity Matrix */
74 float defaultAAMatrix[20][20] = {
75 { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0},
76 { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3},
77 { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3},
78 { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3},
79 { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1},
80 { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2},
81 { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2},
82 { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3},
83 { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3},
84 { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3},
85 { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1},
86 { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2},
87 { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1},
88 { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1},
89 { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2},
90 { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2},
91 { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0},
92 { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3},
93 { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1},
94 { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}
95 };
96
97
98 /* Alternative matrixes */
99
100 // Nucleotides
101 float alternative_1_NTDegeneratedMatrix[15][15] = {
102 { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
103 { 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
104 { 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
105 { 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
106 { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
107 { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
108 { 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0},
109 { 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0},
110 { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0},
111 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0},
112 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0},
113 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0},
114 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0},
115 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0},
116 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1}
117 };
118
119 #endif