Dear Minh,
as Karen I was wondering whether the input order of the partitions is the same as the order of the numbers in the "partition specific rates" (*.log) output
and whether speed (*.iqtree file) is the same as the "partition specific rates"?
After finding the answer, I checked my data and I could not find the correspondence that I would have expected:
For my data set the *.log file contains the following partition specific rates:
Partition-specific rates: 0.151 0.141 0.236 0.366 0.390 0.381 0.225 0.213 0.517 ....
In the corresponding *.iqtree file I find:
Edge-linked-proportional partition model with separate substitution models and separate rates across sites
ID Model Speed Parameters
1 LG+R3 0.1554 LG+R3{0.823196,0.347324,0.162733,3.17633,0.0140707,14.0142}
2 VT+R3 0.0880 VT+R3{0.888953,0.216238,0.089011,3.39085,0.0220356,22.9607}
3 JTT+R3 0.1972 JTT+R3{0.841837,0.286363,0.133907,3.23114,0.024256,13.4505}
4 JTT+R3 0.3208 JTT+R3{0.682353,0.204336,0.264993,1.82026,0.0526532,7.18312}
5 JTT+R3 0.2231 JTT+R3{0.764902,0.0547832,0.206728,2.21628,0.0283696,17.622}
6 LG+R3 0.4109 LG+R3{0.646799,0.171039,0.328276,2.08465,0.0249248,8.22599}
7 JTT+R4 0.2162 JTT+R4{0.682751,0.151679,0.241186,1.58744,0.0697556,5.37925,0.00630789,21.9312}
8 JTTDCMut+R4 0.2303 JTTDCMut+R4{0.423401,0.0336106,0.398709,0.847233,0.164368,3.20274,0.0135223,8.98831}
9 LG+R4 0.5182 LG+R4{0.337071,0.0207592,0.399248,0.551705,0.221075,2.15266,0.0426058,6.96706}
You wrote that they are exactly the same but might look different due to rounding.
But I do not have this correspondence between the numbers in the rates line and the speed column (3rd column in the *.iqtree file).
The difference cannot be explained by rounding differences, nor by re weighting the numbers.
Well, it looks as if:
- they are not in the same order?
- they are different things?
Many thanks for your help in advance.
Christoph