https://polypompholyx.github.io/tag/phylogenetics/Recent content in phylogenetics on PolypompholyxHugoen-GBExcept where otherwise noted, content on this site is licensed under a Creative Commons CC-BY-SA-3.0 licence, Steve CookMon, 23 Mar 2020 11:01:25 +0000https://polypompholyx.github.io/2020/03/pythogenies/Mon, 23 Mar 2020 11:01:25 +0000https://polypompholyx.github.io/2020/03/pythogenies/<p>I had to teach myself a bit of Python recently, so decided to do it by implementing this <a href="https://polypompholyx.github.io/wp-content/uploads/2020/03/parse_phylogeny.txt">parse_phylogeny.py</a> thing (it&rsquo;s uploaded here as a text file). It takes a nice intuitive mark-down for phylogenetic trees (below) and spits out a Newick file (<code>-f nwk</code>), or a <a href="https://en.wikipedia.org/wiki/Template:Clade">Wikipedia clade</a> format (<code>-f wp</code>). It&rsquo;s not amazing (hey, it was my first attempt at Python in anger) and I know there&rsquo;s a bunch of repetitious stuff in the functions that could be lifted out, but whatever. Maybe you&rsquo;ll find a use for it.</p>