4/1/2024 0 Comments GTR Evolution windowed modeAnd we choose ’16s_filtered.out’ as part of all result file names. As explained above, we’ll use the GTRCAT model, and the ‘-f a’ option to run a ML search and bootstraps in the same run. Only for the reason that I find this easier than remembering all necessary options before the run. We’ll start with as little command line options as possible, and learn along the way which other options we need. So, let’s try to run a ML search with bootstaps for the 16s sequence data, using the alignment that was filtered with BMGE, the file called 16s_filtered.phy. This is fine if you don’t need bootstrap support values, however we would like to have these, so we choose ‘-f a’ to run a search for the ML tree and a rapid bootstrap analysis in one run.Įxercise 1: Produce an ML phylogeny of 16s If ‘-f’ is not specified, the ‘new rapid hill-climbing’ algorithm will be used. The RAxML help text shows that a large number of algorithms are implemented in RAxML, which you can choose with the the ‘-f’ option. The author of RAxML, Alexis Stamatakis, strongly and convincingly argues against the use of the proportion of invariable sites (the +I) in the manual of RAxML 7.04 (on page 20), so we’ll focus only on the GTRCAT model in this exercise (that said, if you browse through the RAxML help text, you may notice the newly implemented ASC_GTRCAT and ASC_GTRGAMMA models which correct for ascertainment bias in SNP data, and could prove very useful, but will not be covered here). Of these, the latter two are similar to GTRGAMMA, but are computationally a lot faster (in case you want to read up on it later, Paul Lewis has posted a few slides to explain the benefits of the GTRCAT model here). As RAxML is designed for large datasets, the choice of substitution models for nucleotide sequences is limited to rather parameter-rich models of the GTR family, such as GTR+Gamma, GTR+Gamma+I, GTRCAT, and GTRCAT+I. Where ‘sequenceFileName’ and ‘outputFileName’ would have to be replaced with the actual sequence and output file names, and a substitution model would have to be chosen to replace ‘substitutionModel’ (note that for our installation, we start the program with ‘raxml’, not ‘raxmlHPC’, only because we named it that way). RaxmlHPC -s sequenceFileName -n outputFileName -m substitutionModel Close to the top, you’ll see that raxml could be started as easily as Scroll back up to the beginning of the RAxML help text. Next, have a look at the impressive help text of RAxML: (if you see ‘/usr/local/bin/raxml’, things are looking good) Using this console window, navigate to the directory for the RAxML activity: Please make sure that you are logged in to the Workshop’s Amazon Machine Image (AMI) using a console window of either the Terminal application (if you’re on Linux or Mac OSX), or PuTTY (if you’re on Windows). We are going to work with the 16s and rag1 alignments that we built during the Multiple Sequence Alignment exercise, and we will produce bootstrapped ML phylogenies for both alignments. You will learn how to bootstrap Maximum Likelihood (ML) trees in order to assess node support, and how to partition alignment files to allow different substitution models for different regions of the alignment. This exercise is supposed to teach you only the most important functions of RAxML. Exercise 2: Produce an ML phylogeny of rag1.Exercise 1: Produce an ML phylogeny of 16s.
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