I used a strategy by partitioned my dataset (13500 pb * 150 species) by gen and by codon to Protein coding Genes, and one by each rRNA with model_selection : bic and search: greedy. All was ok with the partitionFinder run, and Iqtree, Mrbayes, RaxML analysis. However, to my Beast analysis (using the same partition scheme and 7 calibration points) I cannot arrive to optimize my ESS values after several N° of generations. I supposed it could arrive one day running several analysis and many hr in a cluster. Do you believe that optimize the number of generation could help to optimize the Beast analysis?
What could be the best strategy? Grouping the partition by gen, or by position? or by position and same model ? Or this does not have any sense.
Subset | Best Model | # sites | subset id | Partition names
1 | GTR+I+G | 777 | aa6d08870474a261954d433ad287322a | 12S
2 | GTR+I+G | 1137 | c770cc808857d12eb2d67da7e0758b9b | 16S
3 | GTR+I+G | 1112 | 2ef2eb84dc48341275890c9886e931cd | COII_pos1, ATP6_pos1, COIII_pos1, CYTB_pos1
4 | TVM+I+G | 1014 | 3bd306a9701fb1001b9b06f8625942f2 | COI_pos2, COIII_pos2, ATP6_pos2
5 | TVM+G | 423 | 14af0a2a5e4771d8fcec37f54c19c4fa | ND3_pos3, ATP6_pos3, ATP8_pos3
6 | HKY+I+G | 70 | 09c06b283a6ba155b862fbbb38eeaae7 | ATP8_pos1
7 | GTR+I+G | 283 | 604c00155ccf4a0be8e7dbd1ec888904 | ND6_pos2, ATP8_pos2
8 | GTR+I+G | 517 | 63e10bda2d363c9dee5e81713c85b4ae | COI_pos1
9 | GTR+I+G | 752 | 2b5edf5b945982971c25c94bf9a8fc9f | COI_pos3, COII_pos3
10 | GTR+I+G | 615 | 97a01e0ce67a8045a0482aad57a39f0e | COII_pos2, CYTB_pos2
11 | TIM+G | 265 | e98e1a37d5da6b8c54cd5707f0eafde4 | COIII_pos3
12 | TIM+I+G | 380 | ed77f53d9829f38e52853f1e541a6764 | CYTB_pos3
13 | GTR+I+G | 1455 | cc75992d6172e44b09acff9311e955e3 | ND5_pos1, ND1_pos1, ND4L_pos1, ND4_pos1
14 | GTR+I+G | 314 | 837d34d1fd73ea9fed0c069125ab885a | ND1_pos2
15 | TVM+I+G | 314 | 719cf8dbcbc87def839e14b6f74e2304 | ND1_pos3
16 | GTR+I+G | 374 | 1f9895b348e888b7f719089ffb41e425 | ND2_pos1
17 | TVM+I+G | 495 | 7b4514749caa8db90ae3ae7e6e46972b | ND2_pos2, ND3_pos2
18 | GTR+G | 374 | c1c9c0bacf26d0bd81b6f430703637e1 | ND2_pos3
19 | GTR+I+G | 334 | 643fb50e0a0911a120c27a203a85bdef | ND6_pos1, ND3_pos1
20 | GTR+I+G | 1141 | 4e0dde062f976253d07b25928fb79cea | ND4L_pos2, ND4_pos2, ND5_pos2
21 | TIM+I+G | 101 | d59867060c15e1b8554ccb066da1647e | ND4L_pos3
22 | TRN+I+G | 1040 | 276ad8fb996a1e06214eedd85c87439a | ND5_pos3, ND4_pos3
23 | HKY+G | 213 | 15994501a9ddd135de599d0ba39dd87c | ND6_pos3