{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# ipyrad-analysis toolkit: RAxML\n", "\n", "RAxML is one of the most popular tools for inferring phylogenetic trees using maximum likelihood. It is fast even for very large data sets. The documentation for raxml is huge, and there are many options. However, I tend to use the same small number of options very frequently, which motivated me to write the `ipa.raxml()` tool to automate the process of generating RAxml command line strings, running them, and accessing the resulting tree files. The simplicity of this tool makes it easy to incorporate into other more complex tools, for example, to infer tress in sliding windows along the genome using the `ipa.treeslider` tool.\n", "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Required software" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# conda install ipyrad -c conda-forge -c bioconda\n", "# conda install raxml -c conda-forge -c bioconda\n", "# conda install ipcoal -c conda-forge" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import ipyrad.analysis as ipa\n", "import toytree\n", "import ipcoal" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Simulate example dataset" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "wrote concat locus (10 x 10000bp) to /tmp/raxtest.phy\n" ] }, { "data": { "text/html": [ "