Michał Ciach

Species tree node labelling

4

Hi, It seems that, after setting the OL parameter to 1, the internal nodes of the species tree in s_tree.trees file are numbered in inorder, while the same nodes in...

Zero-intensity measurements in experimental spectrum cause a shift of noise in results of `estimate_proportions`. Note: zero-intensity measurements are needed for profile spectra to properly handle peak boundaries. Example: ``` T1...

Spectra contain a boolean label `empty` which has an odd behavior. This causes problems with `Spectrum.merge_confs()` method, because it checks this attribute. Example: ```` T = Spectrum(confs=[(1.0, 1), (1.01, 1)])...

Hi, I've noticed that the values stored as node labels are not handled properly during rerooting. Does your software handle other formats of branch support values, e.g. in square brackets...