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57 lines
2.4 KiB
C++
57 lines
2.4 KiB
C++
// simulate positions with dependence 2013 09 22 Eli Levy Karin
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/*
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This code receives a tree file and simulates sequences accordingly using:
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simulateTree st1(treeIn, *_sp, alph);
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st1.generate_seq(num_pos_with_same_k);
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which were written by another beloved group member.
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Its feature is to simulate co-evolution between pairs of positions of binary data. Basic logic:
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1. the basic concept is to use the regular independent model with 4 states to code a dependent model with 2 states.
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thus, all possible pairs of dada: 00, 01, 10, 11 are coded into A, C, G, T
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2. dependency between possitions can be described as a tendency to have the same character (that is: 00 or 11). with this model we can accelerate
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the rate of evolution when an "unstable" state occures (rate increases when 01 or 10)
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For more details, please see http://copap.tau.ac.il/benchmark.php and
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Ofir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein and Tal Pupko (2013)
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CoPAP: Co-evolution of Presence-Absence Patterns.
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Nucleic Acids Research 2013; doi: 10.1093/nar/gkt471
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Eli Levy Karin, 2013
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*/
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#ifndef ___SIM_WITH_DEP
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#define ___SIM_WITH_DEP
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#include <string>
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#include <iostream>
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#include "tree.h"
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#include "alphabet.h"
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#include "nucleotide.h"
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#include "simulateTree.h"
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#include "trivialAccelerator.h"
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#include "uniDistribution.h" // distribution of rates across sites
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#include "generalGammaDistributionPlusInvariant.h"
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#include "generalGammaDistribution.h"
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#include "fastaFormat.h"
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#include <fstream>
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#include "gtrModel.h"
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#include <sstream>
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namespace sim_with_dep {
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double simulate_with_dependence (string treeFile, double PI_1, double init_k, int total_positions, int num_pos_with_same_k, double k_increase, int is_gamma, double alpha, double beta, int num_cat);
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/*
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treeFile - newick format
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total_positions - number of positions to simulate (note that you'll get double this nuber in binary positions)
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num_pos_with_same_k - one can have a different k for parts of the pairs (a gradient, for example).
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Make sure that: (num_pos_with_same_k <= total_positions) and (total_positions % num_pos_with_same_k = 0)
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k_increase - if you decide to simulate with different k's - set by how much k should increase
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is_gamma - if 0 uniDistribution, if 1 generalGammaDistribution
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alpha, beta, number of rate categories are only relevant if is_gamma=1 (otherwise, you can put whatever there)
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*/
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};
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#endif
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