A python phylogeny tracking module

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Project description

phylotrackpy: a python phylogeny tracker

In in silico evolution experiments, we have the luxury of being able to perfectly track the phylogenies of our populations, rather than having to just infer them after the fact. Phylotrackpy is a Python package designed to help you do so as efficiently as possible.

Features

Ability to prune out taxa that are extinct and have no extant descendants (to keep memory use under control)
Flexible control of how taxa are defined (e.g. by genotype, by phenotype, by trait, or by something more complex)
Highly efficient (implemented in C++ under the hood)
Includes various phylogenetic topology metrics

How to use

There are three main steps in using phylotrackpy:

Construct a Systematics object
Notify the systematics object whenever anything is born
Notify the systematics object whenever anyything dies

For more detailed instructions, see the documentation

Installation

Phylotrackpy is available through pip:

pip install phylotrackpy

Project details

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Project links

Homepage

GitHub Statistics

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Release history Release notifications | RSS feed

0.2.0

Mar 1, 2024

0.1.18

Dec 27, 2023

0.1.17

Nov 22, 2023

0.1.16

Jul 23, 2023

0.1.15

Jul 23, 2023

0.1.14

Jul 22, 2023

0.1.13

Mar 10, 2023

0.1.12

Mar 9, 2023

This version

0.1.5

Mar 7, 2023

0.1.1

Feb 24, 2022

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MD5	`2aa4726b6ad2254476dcb889b25028e6`
BLAKE2b-256	`b4e00e086db026db460f2f4a62d1ce3fa7442ff617a48732d341a2613e2e2384`

Hashes for phylotrackpy-0.1.5-cp39-cp39-win_amd64.whl

Hashes for phylotrackpy-0.1.5-cp39-cp39-win_amd64.whl
Algorithm	Hash digest
SHA256	`4dc5b946e81451042fd225e24f95101d981d0ab329cd604aa43e85ea889ab985`
MD5	`9d905b4efd07c66cc5e66c99e9c5e946`
BLAKE2b-256	`e46caf1df5a860044fb486a347cdc3d15fb5ad6eb56da2821e41a0f6c2348484`

Hashes for phylotrackpy-0.1.5-cp39-cp39-win32.whl

Hashes for phylotrackpy-0.1.5-cp39-cp39-win32.whl
Algorithm	Hash digest
SHA256	`f2ad01b681a83e5d997fdeaad8b997c692d25e9837b3552e059075495735a840`
MD5	`eaf966f0b4417909487c9b70a4dc1e56`
BLAKE2b-256	`86191f79bfa0d6e58f987d0c95df9fe055c599cc6a29ff9e594a49be698f3c59`

Hashes for phylotrackpy-0.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`65a60f74b29d7badd0a2b11eafed37034996e6f0fc3713eb74570f0fd9be699f`
MD5	`b749c0e07eb24fdab61a6eaa8bd06be2`
BLAKE2b-256	`a8cff8c70d49d47576282b29f1203bafca86b6469e48ccb17da6d4d40cb68f12`

Hashes for phylotrackpy-0.1.5-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for phylotrackpy-0.1.5-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`4103cf674bb516bf37affd76e70d695312a183263f1ac954e773ea26f7f13df6`
MD5	`66ab7fe26c184d4fb1d6cb2a9f004744`
BLAKE2b-256	`bfc8aea9b342ea7babe9fb2119dc62b72cc86366ea33813897098e337f49f6ba`

Hashes for phylotrackpy-0.1.5-cp39-cp39-macosx_10_9_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`cc41a80748ebc749fc47d707bdba903c5c5e67dbb8bda78a1406e3652d368d54`
MD5	`5617c5ab03086018757a93eb456b1bb0`
BLAKE2b-256	`454e7ed37630da7e0146ca6e8230feaad644c73a0f2ef69d63785f62f12b7252`

Hashes for phylotrackpy-0.1.5-cp38-cp38-win_amd64.whl

Hashes for phylotrackpy-0.1.5-cp38-cp38-win_amd64.whl
Algorithm	Hash digest
SHA256	`bbf1765bceab9b401e5572512b4c9c679b014d5cb6cca33ffa01692d327a20f6`
MD5	`9070a064398a92de3145579af1d67ee2`
BLAKE2b-256	`7273cacc086e25f44d73914f727132fa4357761d51b1b312c22110c1d28bc7a2`

Hashes for phylotrackpy-0.1.5-cp38-cp38-win32.whl

Hashes for phylotrackpy-0.1.5-cp38-cp38-win32.whl
Algorithm	Hash digest
SHA256	`194c61e6f84cf4053d067d3146b30555f1e3ba0b274b5bf3e6813f8733c60bae`
MD5	`ff4045b0bc923ef0b8a4ffc11b176b43`
BLAKE2b-256	`e3a85294eec3aa637baafc2f71c50eea12565cb3a0a2b61498e049066156356b`

Hashes for phylotrackpy-0.1.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`4d065e274322ba64e3893d5632a76ff257f16e26e0245ebf3f4df6e03fca1f5f`
MD5	`c3e31a13d7ab440ecba1cbdc8185e368`
BLAKE2b-256	`fdf8f25011192f42cefa2f54755b9fbbf78c60c0bd9f55ff77a222e880caf7fa`

Hashes for phylotrackpy-0.1.5-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for phylotrackpy-0.1.5-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`8ea35e13c7e17c1a1cf7873f65e1a79d04548eb6dc0b069f21c51aadd20b6318`
MD5	`f4a21b89409b2e7cfac993e2fd510c9a`
BLAKE2b-256	`b16d9e38b6e6fbb3e8c7b858484b7e8d9737d3953230a917e6e158804946343c`

Hashes for phylotrackpy-0.1.5-cp38-cp38-macosx_10_9_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`76cf4243ebacb41c270a51e3e917ebea0663d478310d01f33ffe7bf2fa40646c`
MD5	`6ea4e3a632d163e7cda3d4e49cec8ded`
BLAKE2b-256	`53c4a80e9d920ada917ab399b14e0a4c9f050c9860a169ae52cd320f5ab59113`

Hashes for phylotrackpy-0.1.5-cp37-cp37m-win_amd64.whl

Hashes for phylotrackpy-0.1.5-cp37-cp37m-win_amd64.whl
Algorithm	Hash digest
SHA256	`355c55d377aacbfd8c448d8ac0222f9059ce0927ddb425a1a558ed5f69f802df`
MD5	`4c62ee125ab70dd58e0f0fe5078d5a61`
BLAKE2b-256	`8f8b75da3a59d53ef4fdf2581322f97699f728ad32af0c7da48b7359d0d3964f`

Hashes for phylotrackpy-0.1.5-cp37-cp37m-win32.whl

Hashes for phylotrackpy-0.1.5-cp37-cp37m-win32.whl
Algorithm	Hash digest
SHA256	`49a62310bf4b3d429268a97ceaf94df69d7745dcbcca78940cc056fe58619dc1`
MD5	`25d0e7052c9cf6922e6ffd8f0d190ee7`
BLAKE2b-256	`cb8605da45bb785cdfed6be52f42608d038a102b0a896c513ea862b59ad235d6`

Hashes for phylotrackpy-0.1.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`431766a2e84e12c7ec3a5a04f8859f79e336e8a4627f0ae5912672666a76071e`
MD5	`f496762fa8982469bb1b67b91769535b`
BLAKE2b-256	`36dfd4acc9b496e1f6586eebec8d097ca959692877b92233aa7f0edb5f5a7512`

Hashes for phylotrackpy-0.1.5-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for phylotrackpy-0.1.5-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`1d9583ff685c7ef09bda35c630df8ba086cb1faf9e78000c4ee2ef450c7a660f`
MD5	`1a6976849b40dbbe0b93a2be1dfbdba3`
BLAKE2b-256	`d866fa5857e3f90eda6251bc54e25048a648bb2e4deccd05a9b868a3faca1790`

Hashes for phylotrackpy-0.1.5-cp37-cp37m-macosx_10_9_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp37-cp37m-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`d9e216a85b9d2c56d76af2d0183d8bd7f408137e26ed6d65bd4e745eed249022`
MD5	`45624963af9914234081fb2b537dd5d8`
BLAKE2b-256	`ef46c8e4f7a50441c1a2763ce3ba2fe6371ae70111f951d1baefda80face093f`

Hashes for phylotrackpy-0.1.5-cp36-cp36m-win_amd64.whl

Hashes for phylotrackpy-0.1.5-cp36-cp36m-win_amd64.whl
Algorithm	Hash digest
SHA256	`93f62df018802e5f1f090e270cb245148f8fd58644418bbcc26e1153085c88e7`
MD5	`d3f790b99e87d0537f9414a9dd994cbc`
BLAKE2b-256	`125818b1adbe21fc3a4343ed296b0cba3320bc1da6fbb7442444b51962824ec9`

Hashes for phylotrackpy-0.1.5-cp36-cp36m-win32.whl

Hashes for phylotrackpy-0.1.5-cp36-cp36m-win32.whl
Algorithm	Hash digest
SHA256	`623f53b4f0415fff24e8f4447b180be67652e8461fe7650573fe55c0ca3c4800`
MD5	`7821416e84c6c272fed915c10abd1420`
BLAKE2b-256	`2b5e2ed5d020448b54e8ba6a31bb8256c311e80295adb2c2e000821e32d53ce4`

Hashes for phylotrackpy-0.1.5-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`b3959effbe497921759f624dea31d25d1108e38beb36234a182065db0b178608`
MD5	`7adf8092f6e8653188a1f403fba7036a`
BLAKE2b-256	`d78bd10b5dc16872a818b452184e77479594ee04b074996be99f084a8815e898`

Hashes for phylotrackpy-0.1.5-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for phylotrackpy-0.1.5-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`a5ed2a44bdfc274c46c6be10036758954a9a7a37a30efbcf99e918d7614d015a`
MD5	`5cee59ff9fe11115b5afc23b40c6edd7`
BLAKE2b-256	`d5e5944d5127f34252407ee6ef503b67d438c474f6849af4b23e86e6694050e6`

Hashes for phylotrackpy-0.1.5-cp36-cp36m-macosx_10_9_x86_64.whl

Hashes for phylotrackpy-0.1.5-cp36-cp36m-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`9f1ee1f5c443fc271c5404d6dd41a7ba2c687d831c0669d0c477e9d5f9e27e6d`
MD5	`1d3157a43051fc6b385893f5785c25e0`
BLAKE2b-256	`5bfebccf169f886a11ce737d5319cce93c7a15dcda35aaac289e56461125135d`