Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree

Question

[dtejadamartinez]

I have a .orthoxml outputs that are my results from Oma Standalone. To analyze the hierarchical orthologous groups (HOG) stored in OrthoXML files I need to use the Pyham application which requires the ETE toolkit.

I have a linux computer and I work using the command line, but I am new using python and I have not found a way to follow the instructions to perform the steps that Pyham requires.

Could you help me with the instructions to follow from the start?

I have already installed

Python 3.5.2 Qt 5.7.0 PyQT ete3 conda

"The first step is to instantiate a pyham.taxonomy.Taxonomy object by constructing a ete3.Etree object based on the inputted newick tree and assign to each Etree node the related pyham.genome.Genome.

pyham.genome.ExtantGenome are named according to the newick leaves name while pyham.genome.AncestralGenome are either name using the internal node name from the newick tree or the the concatenation of the genome children name"

Thanks,

Answer 1

[Christophe Dessimoz]

The documentation of pyHam can be accessed here: https://github.com/DessimozLab/pyham

There is a tutorial here: http://lab.dessimoz.org/blog/2017/06/29/pyham

Finally, there is now an Application Note introducing the package here: https://doi.org/10.1093/bioinformatics/bty994