{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Canarium GBS: Phylogenetic inference\n",
"### *Federman et al.*\n",
"\n",
"This notebook provides all code necessary to reproduce Phylogenetic analyses for the full data sets performed with raxml and tetrad. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Required software"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"## conda install ipyrad -c ipyrad\n",
"## conda install toytree -c eaton-lab\n",
"## conda install sra-tools -c bioconda\n",
"## conda install entrez-direct -c bioconda\n",
"## conda install raxml -c bioconda"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Imports"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ipyrad v.0.7.20\n"
]
}
],
"source": [
"import toytree\n",
"import toyplot.svg\n",
"import ipyrad as ip\n",
"import ipyrad.analysis as ipa\n",
"print \"ipyrad v.{}\".format(ip.__version__)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Connect to cluster"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"host compute node: [40 cores] on sacra\n"
]
}
],
"source": [
"import ipyparallel as ipp\n",
"ipyclient = ipp.Client()\n",
"ip.cluster_info(ipyclient)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Get SRA Run info"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\r",
"Fetching project data..."
]
},
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" Run | \n",
" spots | \n",
" spots_with_mates | \n",
" ScientificName | \n",
" SampleName | \n",
"
\n",
" \n",
" \n",
" \n",
" | 0 | \n",
" SRR5534921 | \n",
" 12818693 | \n",
" 0 | \n",
" Canarium lamianum | \n",
" SF327 | \n",
"
\n",
" \n",
" | 1 | \n",
" SRR5534922 | \n",
" 5675773 | \n",
" 0 | \n",
" Canarium longistipulatum | \n",
" D12950 | \n",
"
\n",
" \n",
" | 2 | \n",
" SRR5534923 | \n",
" 34404746 | \n",
" 0 | \n",
" Canarium ovatum | \n",
" D14269 | \n",
"
\n",
" \n",
" | 3 | \n",
" SRR5534924 | \n",
" 3382649 | \n",
" 0 | \n",
" Canarium pilicarpum | \n",
" 5573 | \n",
"
\n",
" \n",
" | 4 | \n",
" SRR5534925 | \n",
" 16632442 | \n",
" 0 | \n",
" Canarium obtusifolium | \n",
" SF228 | \n",
"
\n",
" \n",
"
\n",
"