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EukPhylo/PTL2/Scripts-GRID/trimal-trimAl/source/values.h
Katzlab dd76ab1d12 Added PTL2 Scripts 
These are PTL2 files from Auden 2/9
2023-02-14 11:20:52 -05:00

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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
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