\n",
"\n",
"The `tetrad` tool is a framework for inferring a species tree topology using quartet-joining on large unlinked SNP data sets. It is particularly optimized for RAD-seq type datasets that are likely to involve a lot of missing data. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Load libraries"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
"# conda install ipyrad -c conda-forge -c bioconda\n",
"# conda install tetrad -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 a random tree with 20 tips and crown age of 10M generations"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"