This repo contains the phylogenetic analysis code used in the publication xxxxxxx.
The data is from the All Species Living Tree Project and consists of two files: LTPs123_LSU_tree.newick and LTPs123_LSU_aligned.fasta
The code to make some pretty plots and entropy calculations based on these data can be found in: LTP_sequence_parsing.ipynb
This code is written in python 3.0 and requires jupyter notebook. Other requirements are relatively standard scientific packages (scipy, numpy, pandas) as well as Biopython.
Questions can be addressed to [email protected]