Unexplained base content of sequence alignment generated under UNREST model #160
Description
I am trying to generate sequence alignments under the UNREST model. However, I am puzzled by the base content of the generated sequences.
I run the following command
iqtree2 --alisim alignment_vwxy-1000_unr-31331333333-25252525 -t vwxy_1000.nwk -m UNREST{3.0/1.0/3.0/3.0/1.0/3.0/3.0/3.0/3.0/3.0/3.0}+F{0.25/0.25/0.25/0.25} --length 25000 -redo
((V:1.0,W:1.0):0.0,(X:1.0,Y:1.0):0.0); # vwxy_1000.nwk
I expected that the generated sequence containing equal amounts of A, T, C and only a small amount of G. In fact, the sequence contained small amount of G, but a larger amount of T than A or C.
| Base | Content (%) |
|---|---|
| A | 28.6 |
| C | 27.7 |
| G | 11.3 |
| T | 32.3 |
In addition, I ran three commands to verify the behavior of the UNREST model.
iqtree2 --alisim alignment_vwxy-1000_jc -t vwxy_1000.nwk -m JC --length 25000 -redo
iqtree2 --alisim alignment_vwxy-1000_gtr-11111-25252525 -t vwxy_1000.nwk -m GTR{1.0/1.0/1.0/1.0/1.0}+F{0.25/0.25/0.25/0.25} --length 25000 -redo
iqtree2 --alisim alignment_vwxy-1000_unr-11111111111-25252525 -t vwxy_1000.nwk -m UNREST{1.0/1.0/1.0/1.0/1.0/1.0/1.0/1.0/1.0/1.0/1.0}+F{0.25/0.25/0.25/0.25} --length 25000 -redo
My understanding is that these commands should be equivalent. However, only the UNREST model showed a base content that deviated significantly from the expected value.
| JC | GTR | UNREST | |
|---|---|---|---|
| A | 25.1 | 25.2 | 28.0 |
| C | 25.1 | 24.7 | 24.1 |
| G | 24.9 | 25.0 | 22.2 |
| T | 24.9 | 25.2 | 25.6 |
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