data block missing in the results

[Paola María Sánchez Martínez]

Hi people

So, I have "data blocks" in my input file, but the program doesn't read it. I checked the format of the files and I can find the error. My matrix is bigger, but the analysis neither works with these files. Look at the data blocks in the .cfg, but look at the results in the best scheme file...

Please, help me! I´m sure is a small detail... I hope

Thanks

Paola

[Rob Lanfear]

Hi Paola, 

It all looks fine to me - but maybe I'm not understanding. 

You have this in your config file:

```
[data_blocks] 

cytb_pos1 = 1 - 303\3; 

cytb_pos2 = 2 - 303\3; 

cytb_pos3 = 3 - 303\3;
```

and in your best scheme file the best scheme joins all of these together

```

Subset | Best Model | # sites | subset id | Partition names 1 | GTR+I+G | 303 | c5451ff6157270a8d2caeebf094fa94f | cytb_pos1, cytb_pos2, cytb_pos3                                                                      

```

All three of your partitions are in there, so I'm not quite sure what you think the problem is.

Of note though - you should probably try using linked branchlengths for this too, since linked branchlengths is usually the best model (see e.g. https://academic.oup.com/mbe/article/37/4/1202/5673393?login=true)

Do let me know if I totally misunderstood though!

Rob

[Yu Sun]

Hi Rob,

I'm curious if this software can partition protein-coding amino acids and nucleotides of tRNAs genes for partitioning and calculating models? Thank you.

Best,

Yu Sun

Rob Lanfear <rob.l...@gmail.com> 于2021年10月21日周四 下午5:39写道：

--
You received this message because you are subscribed to the Google Groups "PartitionFinder" group.
To unsubscribe from this group and stop receiving emails from it, send an email to partitionfind...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/partitionfinder/1bf43e44-1dc5-4135-8ba8-24dd586cfdfbn%40googlegroups.com.

[Rob Lanfear]

Hi Yu,

You can provide any data blocks you like, and PartitionFinder will try merging them to improve the AIC/AICc/BIC scores. However, you can't mix amino acid and dna/rna data. 

Rob

[Yu Sun]

Okay, I got it. Thank you.

Yu

On Nov 26, 2021, at 3:21 AM, Rob Lanfear <rob.l...@gmail.com> wrote:

the