Mercurial > repos > padge > trimal
view trimal_repo/source/values.h @ 0:b15a3147e604 draft
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
| author | padge |
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| date | Fri, 25 Mar 2022 17:10:43 +0000 |
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/* ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** trimAl v1.4: a tool for automated alignment trimming in large-scale phylogenetics analyses. 2009-2015 Capella-Gutierrez S. and Gabaldon, T. [scapella, tgabaldon]@crg.es This file is part of trimAl. trimAl is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, the last available version. trimAl is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with trimAl. If not, see <http://www.gnu.org/licenses/>. ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** ***** */ #ifdef SIMMatrix /* Characters used for different alignments type */ char listNTSym[6] = "ACGTU"; char listAASym[21] = "ARNDCQEGHILKMFPSTWYV"; char listNTDegenerateSym[16] = "ACGTURYKMSWBDHV"; /* Characters used to indicate indeterminations */ char protein_wildcards[3] = "BX"; /* Pyrrolysine: 'O' > 'TAG' */ /* Selenocysteine: 'U' > 'TGA' */ char protein_alternative_aminoacids[3] = "UO"; /* Default Identity Matrix for Canonical Nucleotides */ float defaultNTMatrix[5][5] = { {1, 0, 0, 0, 0}, {0, 1, 0, 0, 0}, {0, 0, 1, 0, 0}, {0, 0, 0, 1, 0}, {0, 0, 0, 0, 1} }; float defaultNTDegeneratedMatrix[15][15] = { /* A: adenosine (A) C: cytidine (C) G: guanine (G) T: thymidine (T) U: uridine (U) * R: purine (G | A) Y: pyrimidine (C | T/u) K: keto (G | T/u) M: amino (A | C) S: strong (G | C) * 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) */ { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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}, { 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.} }; /* BLOSUM62 Similarity Matrix */ float defaultAAMatrix[20][20] = { { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0}, { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3}, { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3}, { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3}, { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1}, { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2}, { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2}, { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3}, { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3}, { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3}, { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1}, { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2}, { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1}, { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1}, { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2}, { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2}, { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0}, { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3}, { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1}, { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4} }; /* Alternative matrixes */ // Nucleotides float alternative_1_NTDegeneratedMatrix[15][15] = { { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0}, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1} }; #endif