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Start Your TrialThe long term evolution of DNA can be modelled using the coalescent. The Markov chain simulation technique developed by Griffiths and Tavaré can be used to produce likelihood estimates for DNA sequence data under the infinitely-many-sites model. The program genetree will calculate not only likelihoods but also simulate likelihood surfaces for parameter estimationin subdivided populations with or without population growth. A whole host of statistics can be calculated including times to the most recent common ancestor, probabilities of the location of the most recent common ancestors, times to the different mutations and the probabilities of these having occurred in the various subpopulations.
This command lines is currently supported:
Generate all possible rooted trees: genetree infile.dat -z
Then Run results for all rooted trees: genetree infile_dat.# 1.4 100 72189 -m infile.mig > infile.out_100
These could be supported on request
Allow for different population sizes: genetree infile_dat.# 9.7 100000 72189 -p infile.size -m infile.mig>infile.out0.1_100000
Allow for different population sizes and 'extra' populations: genetree infile_dat.# 9.7 100000 72189 -p pop.dat -s 3 -m infile.mig > infile.out_100000
Generate ages of mutations for tree with the highest root probability: genetree infile_dat.3 7.5 100 72189 -x 100000 -m infile.mig -o 4 >infile_age.3
Most comprehensive output: genetree infile_dat.51 9.7 1000000 72189 -m infile.mig -o 7 >infile_age.51_1000000
Simulate theta: genetree infile_dat.50 7.5 1000 72189 -x 100000 -m infile.mig -f surf.31_1000 -g 7.0 20 150 -2 >surfout.31_1000
tool=GENETREE_XSEDE
Input files:
infile_ = input_file.txt
Parameters:
runtime_ - Float - Maximum Hours to Run (default 0.25)
theta_val_ - Float - Specify a value for theta.
run_val_ - Integer - Specify the number of runs
seed_val_ - Integer - Specify a seed value
multifile_sum_ - Switch - Generate multifile summary (-l)
num_segsites_ - Integer - Number of segregating sites + 1 (-Z)
max_eventspersim_ - Integer - Maximum events in one simulation run (default - 500) (-x)
max_anc_ - Integer - Maximum types in the ancestry of the sample (-y)
output_level_ - Excl - Output Level (-o); 1 likelihood; 2 show tree; 3 TMRCA; 4 age of mutations; 5 MRCA distribution in subpopulations; 6 mutation distribution in subpopulations; 7 subpopulation TMRCA
outfile_name_val_ = String Specify the output file name