I am trying to parse a .nwk file output from FastTree software. Here is a piece of it as an example.
(ID126413:0.01185,ID031253:0.01551)0.745:0.01406)0.979:0.08500)0.978:0.09525)0.862:0.04279)0.842:0.05587)0.386:0.02730)0.714:0.05495,(ID125859:0.09326,(ID945485:0.00114,(ID993534:0.00360,ID599602:0.00055)1.000:0.13792)0.379:0.17271)0.997:0.18650)0.874:0.07213)0.789:0.01847)0.895:0.03799);
I understand that the length of the branches follow the ID of the tree node. So I understand what the first bold means in my example, but what does the 2nd bolded item mean? What is meant by 0.874:0.07213 ? Can someone please explain this? I am having hard time figuring how to parse this if some of the "nodes" get returned as what looks like branch lengths. Is 0.874 a node name? That seems silly/wrong.
Note, this is how all of my trees are returning from FastTree, which is a highly cited phylogenetic tree software.
Thank you!
http://evolution.genetics.washington.edu/phylip/newicktree.html
Thank you, that helped a lot to point me in the right direction. So if I want to do some experimentation with branch lengths, do the bootstrap value's branch lengths matter or can I essentially ignore them? I.e. If I modify the branch length of tips or branch lengths of non-tips, do I just ignore the bootstrap value's branch lengths or do they count as the tips or non-tips? I didn't add this to my original question, because I had no clue what those values were. Thanks for your time!
If all you want to do is rescale all the branch lengths then all should be fine. As the branch length represents the number of mutations per site, changing it in some branches and not others would imply a different sequence alignment than the one you started with and thus could also affect the bootstrap values. The bootstrap values represent the statistical support for the branches so if you change the topology of the tree, they become meaningless.