I've run it three times to try different parameters, but it stops changing after running for a short while. Please help me understand how to fix this. Is there a problem with the sequence or the parameters?
6471000 -- (-192324.911) [-190903.882] (-191836.670) (-203192.846) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:24:32 6472000 -- (-192324.911) [-190903.882] (-191836.670) (-203199.097) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:23:56 6473000 -- (-192324.911) [-190903.882] (-191836.670) (-203206.485) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:23:22 6474000 -- (-192324.911) [-190903.882] (-191836.670) (-203186.976) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:22:47 6475000 -- (-192324.911) [-190903.882] (-191836.670) (-203176.349) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:22:12 Average standard deviation of split frequencies: 0.143548 6476000 -- (-192324.911) [-190903.882] (-191836.670) (-203174.778) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:21:37 6477000 -- (-192324.911) [-190903.882] (-191836.670) (-203190.326) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:21:02 6478000 -- (-192324.911) [-190903.882] (-191836.670) (-203201.748) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:20:27 6479000 -- (-192324.911) [-190903.882] (-191836.670) (-203196.704) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:19:52 6480000 -- (-192324.911) [-190903.882] (-191836.670) (-203173.040) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:19:18 Average standard deviation of split frequencies: 0.143548 6481000 -- (-192324.911) [-190903.882] (-191836.670) (-203178.787) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:18:43 6482000 -- (-192324.911) [-190903.882] (-191836.670) (-203151.441) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:18:08 6483000 -- (-192324.911) [-190903.882] (-191836.670) (-203159.321) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:17:33 6484000 -- (-192324.911) [-190903.882] (-191836.670) (-203156.963) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:16:58 6485000 -- (-192324.911) [-190903.882] (-191836.670) (-203142.242) * (-192291.336) (-195396.079) (-197058.880) [-190667.824] -- 36:16:24 Average standard deviation of split frequencies: 0.143548
If the avg SE is not going down then the runs are failing to converge which means that there is too little phylogenetic information in the sequence alignment.
Note that the likelihood scores have not changed either over the 11,000 generations you show here,
Six million plus generations should result in multiple lowering plateaus of better fit. But this does not seem to be happening.
If you wish you could send me the alignment and I could assess whether the data is possibly informative.
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