{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Applying a discrete-time, non-stationary nucleotide model\n", "\n", "We fit a discrete-time Markov nucleotide model. This corresponds to a Barry and Hartigan 1987 model." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
key | \n", "lnL | \n", "nfp | \n", "DLC | \n", "unique_Q | \n", "\n", "\n", "
---|---|---|---|---|
\n", " | -6941.4684 | \n", "135 | \n", "True | \n", "\n", " |
log-likelihood = -6941.4684
\n", "number of free parameters = 135
\n", "edge | \n", "motif | \n", "motif2 | \n", "psubs | \n", "\n", "\n", "
---|---|---|---|
Galago | \n", "T | \n", "T | \n", "0.8751 | \n", "
Galago | \n", "T | \n", "C | \n", "0.0649 | \n", "
Galago | \n", "T | \n", "A | \n", "0.0409 | \n", "
Galago | \n", "T | \n", "G | \n", "0.0192 | \n", "
Galago | \n", "C | \n", "T | \n", "0.1126 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "
edge.3 | \n", "A | \n", "G | \n", "0.0055 | \n", "
edge.3 | \n", "G | \n", "T | \n", "0.0000 | \n", "
edge.3 | \n", "G | \n", "C | \n", "0.0011 | \n", "
edge.3 | \n", "G | \n", "A | \n", "0.0039 | \n", "
edge.3 | \n", "G | \n", "G | \n", "0.9950 | \n", "
A | \n", "C | \n", "G | \n", "T | \n", "\n", "\n", "
---|---|---|---|
0.3774 | \n", "0.1763 | \n", "0.2058 | \n", "0.2404 | \n", "
edge | \n", "motif | \n", "motif2 | \n", "psubs | \n", "\n", "\n", "
---|---|---|---|
Galago | \n", "T | \n", "T | \n", "0.8751 | \n", "
Galago | \n", "T | \n", "C | \n", "0.0649 | \n", "
Galago | \n", "T | \n", "A | \n", "0.0409 | \n", "
Galago | \n", "T | \n", "G | \n", "0.0192 | \n", "
Galago | \n", "C | \n", "T | \n", "0.1126 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "
edge.3 | \n", "A | \n", "G | \n", "0.0055 | \n", "
edge.3 | \n", "G | \n", "T | \n", "0.0000 | \n", "
edge.3 | \n", "G | \n", "C | \n", "0.0011 | \n", "
edge.3 | \n", "G | \n", "A | \n", "0.0039 | \n", "
edge.3 | \n", "G | \n", "G | \n", "0.9950 | \n", "
\n", "176 rows x 4 columns
" ], "text/plain": [ "edge motif motif2 params\n", "===================================\n", " edge motif motif2 psubs\n", "-----------------------------------\n", "Galago T T 0.8751\n", "Galago T C 0.0649\n", "Galago T A 0.0409\n", "Galago T G 0.0192\n", "Galago C T 0.1126\n", " ... ... ... ...\n", "edge.3 A G 0.0055\n", "edge.3 G T 0.0000\n", "edge.3 G C 0.0011\n", "edge.3 G A 0.0039\n", "edge.3 G G 0.9950\n", "-----------------------------------\n", "\n", "176 rows x 4 columns" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stats['edge motif motif2 params']" ] } ], "metadata": { "kernelspec": { "display_name": "Python [conda env:c3dev] *", "language": "python", "name": "conda-env-c3dev-py" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.1" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": {}, "version_major": 2, "version_minor": 0 } } }, "nbformat": 4, "nbformat_minor": 4 }