NicolaDM

Thank you very much Theo, that works! Now I get this error though: ValueError: Error: The key column 'node' contains non-unique values in the metadata file. Despite the fact that...

I see - indeed I carelessly added an extra tab at the end of each non-title row. Thanks, I'll fix it!

Indeed I confirm this fixed the problem and now it works - thanks again!

@amkram thank you so much, this looks really cool! I just finished making MAPLE output tree and metadata conforming to the required format, and it seems to work without problems....

MAPLE defines the root nucleotide frequencies as the nucleotide frequencies in the input reference genome. This is an approximation based on the assumption of short divergence from the reference. In...

Yes, this is already implemented: MAPLE will write a nexus output tree when necessary, that is when using option --estimateMAT (which estimates a mutation-annotated tree) or --aBayesPlus (which calculates branch...

If you don't want to wait for me to implement this, a quick solution is to ask MAPLE to create a NEXUS tree (for example using option --estimateMAT ), and...

The meaning is as follows: **RF** This is the number of branches present in one of the two trees but not the other (only branches with length >0.000006 are considered,...

There are a few complications here that need to be ironed out. It is true that the MAPLE format is a lossless compression of an alignment, but only for alignments...

I am currently working on improving the code/algorithm (there is still substantial margin to reduce time and memory demands). At the same time I am in contact with other groups...