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Workflow.txt
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To show:
1. ED is ok for TC sensu Maddison
2. ED is ok for TC TA sensu Tarasov 2019
3. compare ED with HMM through model extension
4. Run multiple runs
#---------------------------------------------
Commnds:
nohup ./rb Morpho_TA_M2.Rev > M2_log.txt &
nohup ./rb Morpho_TA_M3_exp.Rev > M3_log_exp.txt &
nohup ./rb Morpho_TA_SMM_ind.Rev > SMM_ind_log.txt &
nohup ./rb Morpho_TC_L_M5.Rev > M5_TC_L.txt &
ps
find ./ -name '*.tre' -exec cp -prv '{}' '/Users/taravser/Documents/My_papers/Reply2Goloboff/Rev/MorphoModels/run_2_trees' ';'
nohup ./rb Morpho_TA_M3_exp.Rev > M2_log.txt &
nohup ./rb Morpho_TA_M6_exp.Rev > M2_log.txt &
nohup ./rb Morpho_TA_SMM_ind.Rev > M2_log.txt &
nohup ./rb Morpho_TA_SMM_sw.Rev > M2_log.txt &
#---------------------------------------------
Variants of ED a/p:
1. Q: diff EQ, pi: equal, Npar=3
rates := [ [ 0.0, q[2], 0.0, 0.0],
[ q[1], 0.0, q[2]*0.5, q[2]*0.5],
[ q[1], q[1], 0.0, q[3]],
[ q[1], q[1], q[3], 0.0]]
2. Q: diff EQ, pi: equlibrium, Npar=3
rates := [ [ 0.0, q[2], 0.0, 0.0],
[ q[1], 0.0, q[2]*0.5, q[2]*0.5],
[ q[1], q[1], 0.0, q[3]],
[ q[1], q[1], q[3], 0.0]]
3. Q: q=1; pi: equal, Npar=1
a pa pp0 pp1
a -1 1 0 0
pa 1 -3 1 1
pp0 1 1 -3 1
pp1 1 1 1 -3
pi=(1/4, ...)
4. Q: q=1; pi: equlibrium, Npar=1
a pa pp0 pp1
a -1 1 0 0
pa 1 -3 1 1
pp0 1 1 -3 1
pp1 1 1 1 -3
5. Q: q=1, pi: Inferred, Npar=4
a pa pp0 pp1
a -1 1 0 0
pa 1 -3 1 1
pp0 1 1 -3 1
pp1 1 1 1 -3
6. Q: -q=1; pi: equal, Npar=1
[ [ 0.0, 1.0, 0.0, 0.0],
[ 1/3, 0.0, 1/3, 1/3],
[ 1/3, 1/3, 0.0, 1/3],
[ 1/3, 1/3, 1/3, 0.0]]
7. Q: -q=1; pi: equlibrium, Npar=1
[ [ 0.0, 1.0, 0.0, 0.0],
[ 1/3, 0.0, 1/3, 1/3],
[ 1/3, 1/3, 0.0, 1/3],
[ 1/3, 1/3, 1/3, 0.0]]
8. Q: -q=1; pi: Inferred, Npar=4
[ [ 0.0, 1.0, 0.0, 0.0],
[ 1/3, 0.0, 1/3, 1/3],
[ 1/3, 1/3, 0.0, 1/3],
[ 1/3, 1/3, 1/3, 0.0]]
#-----------------------------
Expanded Models
rates := [[0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.0, 0.0],
[1/12, 1/12, 1/12, 1/12, 0.0, 0.0, 1/3, 1/3],
[1/12, 1/12, 1/12, 1/12, 0.0, 0.0, 1/3, 1/3],
[1/12, 1/12, 1/12, 1/12, 1/6, 1/6, 0.0, 1/3],
[1/12, 1/12, 1/12, 1/12, 1/6, 1/6, 1/3, 0.0]]