MAPLE

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output in nexus file

4

Is it possible to convert the output file from .tree format to a .nexus format? Several programs for further analysis require the file to be in nexus format. However, standard...

MarliesJFrancine

Implementing RF calculation

1

When calculating the RF distance between several trees, how are the values "found branches", "missed branches", and "not found branches" calculated? If "found branches" is the number of identical branches...

MarliesJFrancine

How to get nucleotide equilibrium and symmetry matrix

2

Maple can output Q matrix, but can it output nucleotide equilibrium frequency and symmetry matrix. Especially the nucleotide equilibrium frequency. Looking forward to your answer.

fightyy

Extension for Maple format: including insertions

1

In order to allow lossless compression, insertions need to be included in the Maple format. I could find this edge case specified in the preprint. It's easy to do, one...

corneliusroemer

Potential for multi-threading?

1

I assume parts of this algorithm could be parallelized. eg. using `multoprocessing` library What are your plans to do this?

tseemann

- Implement lineage assignments by finding placements for lineage consensus genomes. - Compute SPRTA supports for plausible placements of each lineage. - Parallelize lineage assignments with joblib

trongnhanuit