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Hey there, thanks for the grateful package!
Currently, I am working with the ancestral.pml command. You can see a part of my script here:
```
ml
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I received very strange result of ancestral reconstruction.
1) In the situation where all of the sequences in file given have the same amino acid in one position in the ancestral state in this posit…
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Actually two tests:
- In reconstruction mode, it should return the most likely sequence
- In MCMC mode, it should sample ancestral sequences
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Dear Dr Loytynoja,
This is Francesco from the university of Innsbruck. I'm trying to use prank to align coding mtDNA sequences, but prank is giving me bad jokes. The program works perfectly with th…
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Hi,
I have been using PRANK without any problems for several alignements but for a particular one, PRANK keep crashing with the following error:
```
-----------------
PRANK v.140603:
---------------…
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Hello, I would like to inquire about the input data format. When preparing the config.SFs file, I observed that it is possible to input non-chromosomal data. Consequently, I prepared two datasets.
Th…
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Hi guys,
Thank you very much for such a flexible and powerful library!
I'm interested in developing a web app for general-purpose ancestral sequence reconstruction results visualisation, inspir…
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I wasn't able to test #1333 (which adds support for parsing complex CDSs using GenBank files) because I didn't have translated (AA) fasta files around. This made me wonder why we need the AA sequences…
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Dear Professor,
Now I have CNE file in fasta format, and I can reconstruct the ancestor sequence by PRANK align (By the way, the script I used for the reconstructed ancestor sequence was not Maf2Span…
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Hi @spond @stevenweaver et al
In the old batch files, there used to be an option to turn off rerooting of trees:
```
_DO_TREE_REBALANCE_ = 0;
```
I've tried adding this to the FitMG94.bf, b…