fifteen
=================

(DBA `table_five`)

Experimental library for quick quintet tallying, useful when you have a lot of quintets that somehow you don't want to count yourself.

## Usage

Binary wheels are provided on PyPI

```
python3 -m pip install table_five
```

## API

### `TreeSet`

A treeset is an efficient (i.e., fast parsing) list of tree topologies. The construction is $O(k n \lg n)$ where $k$ is the number of trees and $n$ the number of taxa due to the LCA data structure initialization.

```python
from table_five import TreeSet
trees = TreeSet("path_to_newline_delimited_newicks.tre")
```

#### Quintet Counting

The major API is `tally_sinlge_quintet` returning a list of length 15 containing the empirical
counts of the 15 ADR unrooted quintet topology among the tree-set in $O(k)$ time:

```python
# get counts of the ADR unrooted quintet topologies on taxa '1','2','3','4','5'. Taxa order matters.
treeset.tally_single_quintet(('1','2','3','4','5'))
# obviously you might want to convert it to numpy arrays

# normalize by the number of genes in the tree-set
new_tree_dist = np.asarray(treeset.tally_single_quintet(q_taxa)) / len(treeset)
```


text/markdown; charset=UTF-8; variant=GFM

table-five

runeblaze

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Bad dependency semver

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Bidirectional unicode control characters

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Bin script confusion

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Chrome Extension Content Script

This Chrome extension requests host permissions to access specific websites or domains.

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Chrome Extension Host Permission

This Chrome extension requests permissions to access browser APIs, user data, or system features.

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Chrome Extension Permission

This Chrome extension requests wildcard host permissions that grant broad access to websites.

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Chrome Extension Wildcard Host Permission

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Chronological version anomaly

Project maintainer's SSH key has been compromised.

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Compromised SSH key

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File dependency

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AI-detected potential security risk

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High entropy strings

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Unicode homoglyphs

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HTTP dependency

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Invisible chars

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License Policy Violation

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Network access

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table-five

fifteen

Usage

API

TreeSet

Quintet Counting

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`TreeSet`