BW Indexed in: https://hackmd.io/@hannahkimincompbio/Sk9T_TIBY Writeup leader: Steven WeaverGoogle doc draft 1: https://docs.google.com/document/d/1ERRQVBIyBt_98uRQ7f4EvkgT1L2xJ9pNT-pmHBd1MzA/edit?usp=sharing Google doc draft 2: https://docs.google.com/document/d/1rnGZZZrcIzI6YtZlFgXri3j-mknFHXHonn_kK8h8U_g/edit?usp=sharing Project board: https://github.com/users/stevenweaver/projects/2/views/1 Authors: Sergei Pond, Steven Weaver, Jordan D Zehr, Alexander Lucaci, Hannah Kim, Avery Selberg Institutions: iGEM Potential delivery date: November 19th, 2021 (earliest) Abstract Write last
1/7/2023Your task is to write a Python script which implements a simple Neighbor Joining algorithm for phylogeny inference based on the Jukes Cantor distance, that works reasonably fast for ~20 or so sequences. Do not use "prepackaged" routines from BioPython, other than to read sequence files. Input : a FASTA multiple sequence alignment Output: inferred phylogenetic tree with branch lengths (you can choose the format, but Newick format is standard) For example $python3 NJ.py --msa test.fas ... (((human:0.01, chimp: 0.02): 0.03, gorilla : 0.03, orangutan : 0.03) : 0.01, gibbon : 0.05)
10/24/2022From Drabeck et el "Tall" dataset. This dataset has unusual dimensions: short (30) codons and relatively many (199) sequences. This creates some statistical issues that could potentially be impactful. Many branch lengths are =0 (for example, HyPhy collapses 130 internal tree branches because they are 0). This is not biologically realistic. If possible, it would be better to estimate branch lengths from a longer gene alignment, even if not all species are present. The precision with which non-0 branch lengths are estimated is degraded (likely biased). This could create downstream issues with all method. Methods which draw power from sequence length (e.g. aBSREL, BUSTED, and also PAML), are going to suffer power loss. Basic data exploration.
9/19/2022What you need: A labeled tree. Something like this Parameter settings. We are going to basically ignore everything except ω distributions here Foreground distribution (3 bins) Background distribution (3 bins) Suggested distributions are below. Simulated data. For this, we can use https://github.com/veg/hyphy-analyses/tree/master/SimulateMG94 An example call (notice how the distribution is specified; the one here is ω = 0.1 (weight 0.5), ω = 0.5 (weight 0.3), ω = 1 (weight 0.2)) would be hyphy ~/Development/hyphy-analyses/SimulateMG94/SimulateMG94.bf --model BS-REL --tree marine.txt --output sims/BSREL --replicates 100 --branch-variation bs-rel --omegas 0.1,0.5,0.5,0.3,1,0.2 --omegas-Foreground 0.1,0.5,0.5,0.3,1,0.2
9/16/2022