[](https://coveralls.io/github/HuttleyLab/MutationDiseq)
[](https://github.com/astral-sh/ruff)
# mdeq: a tool for analysing mutation disequilibrium
A manuscript describing the methods will be made available as a preprint soon.
## Installation
```
$ pip install mdeq
```
> **Note**
> `accupy` is an optional package for the most numerically accurate routines involving matrices (e.g. dot products). These routines are explicitly employed for computing the nabla related statistics and are used if this package is installed. Unfortunately it is not easily installed and (at the time of writing) is not under active development.
## The available commands
<!-- [[[cog
import cog
from mdeq import main
from click.testing import CliRunner
runner = CliRunner()
result = runner.invoke(main, ["--help"])
help = result.output.replace("Usage: main", "Usage: mdeq")
cog.out(
"```\n{}\n```".format(help)
)
]]] -->
```
Usage: mdeq [OPTIONS] COMMAND [ARGS]...
mdeq: mutation disequilibrium analysis tools.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
tui Open Textual TUI.
prep pre-process alignment data.
make-adjacent makes sqlitedb of adjacent alignment records.
toe test of existence of mutation equilibrium.
teop between branch equivalence of mutation process test
aeop between loci equivalence of mutation process test
convergence estimates convergence towards mutation equilibrium.
make-controls simulate negative and positive controls
db-summary displays summary information about a db
extract-pvalues extracts p-values from TOE sqlitedb results
extract-nabla-c extracts nabla-c from convergence sqlitedb results
slide generate window sized sub-alignments.
```
<!-- [[[end]]] -->
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"description": "[](https://coveralls.io/github/HuttleyLab/MutationDiseq)\n[](https://github.com/astral-sh/ruff)\n\n# mdeq: a tool for analysing mutation disequilibrium\n\nA manuscript describing the methods will be made available as a preprint soon.\n\n## Installation\n\n```\n$ pip install mdeq\n```\n\n> **Note**\n> `accupy` is an optional package for the most numerically accurate routines involving matrices (e.g. dot products). These routines are explicitly employed for computing the nabla related statistics and are used if this package is installed. Unfortunately it is not easily installed and (at the time of writing) is not under active development.\n\n## The available commands\n\n<!-- [[[cog\nimport cog\nfrom mdeq import main\nfrom click.testing import CliRunner\nrunner = CliRunner()\nresult = runner.invoke(main, [\"--help\"])\nhelp = result.output.replace(\"Usage: main\", \"Usage: mdeq\")\ncog.out(\n \"```\\n{}\\n```\".format(help)\n)\n]]] -->\n```\nUsage: mdeq [OPTIONS] COMMAND [ARGS]...\n\n mdeq: mutation disequilibrium analysis tools.\n\nOptions:\n --version Show the version and exit.\n --help Show this message and exit.\n\nCommands:\n tui Open Textual TUI.\n prep pre-process alignment data.\n make-adjacent makes sqlitedb of adjacent alignment records.\n toe test of existence of mutation equilibrium.\n teop between branch equivalence of mutation process test\n aeop between loci equivalence of mutation process test\n convergence estimates convergence towards mutation equilibrium.\n make-controls simulate negative and positive controls\n db-summary displays summary information about a db\n extract-pvalues extracts p-values from TOE sqlitedb results\n extract-nabla-c extracts nabla-c from convergence sqlitedb results\n slide generate window sized sub-alignments.\n\n```\n<!-- [[[end]]] -->\n\n",
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