Mercurial > repos > padge > trimal

annotate trimal_repo/source/values.h @ 0:b15a3147e604 draft

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