phylodm

Efficient calculation of phylogenetic distance matrices.

https://github.com/aaronmussig/phylodm

Science Score: 54.0%

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CITATION.cff file
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Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary

Keywords from Contributors

mesh sequences interactive hacking network-simulation

Last synced: 6 months ago · JSON representation ·

Repository

Efficient calculation of phylogenetic distance matrices.

Basic Info

Host: GitHub
Owner: aaronmussig
License: gpl-3.0
Language: Rust
Default Branch: main
Homepage:
Size: 653 KB

Statistics

Stars: 48
Watchers: 2
Forks: 3
Open Issues: 3
Releases: 21

Created almost 6 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Citation

🌲 PhyloDM

PhyloDM is a high-performance library that converts a phylogenetic tree into a pairwise distance matrix.

For a tree with 30,000 taxa, PhyloDM will use:

~14GB of memory (94% less than DendroPy)
~1 minute of CPU time (183x faster than DendroPy).

PhyloDM is written in Rust and is exposed to Python via the Python PyO3 API. This means it can be used in either Python or Rust, however, the documentation below is written for use in Python. For Rust documentation, see Crates.io.

⚙ Installation

Requires Python 3.9+

PyPI

Pre-compiled binaries are packaged for most 64-bit Unix platforms. If you are installing on a different platform then you will need to have Rust installed to compile the binaries.

shell python -m pip install phylodm

Conda

shell conda install -c b bioconda phylodm

🐍 Quick-start

A pairwise distance matrix can be created from either a Newick file, or DendroPy tree.

```python from phylodm import PhyloDM

PREPARATION: Create a test tree

with open('/tmp/newick.tree', 'w') as fh: fh.write('(A:4,(B:3,C:4):1);')

1a. From a Newick file

pdm = PhyloDM.loadfromnewick_path('/tmp/newick.tree')

1b. From a DendroPy tree

import dendropy tree = dendropy.Tree.getfrompath('/tmp/newick.tree', schema='newick') pdm = PhyloDM.loadfromdendropy(tree)

2. Calculate the PDM

dm = pdm.dm(norm=False) labels = pdm.taxa()

""" /------------[4]------------ A + | /---------[3]--------- B ---[1]---+ ------------[4]------------- C

labels = ('A', 'B', 'C') dm = [[0. 8. 9.] [8. 0. 7.] [9. 7. 0.]] """ ```

Accessing data

The dm method generates a symmetrical NumPy matrix and returns a tuple of keys in the matrix row/column order.

```python

Calculate the PDM

dm = pdm.dm(norm=False) labels = pdm.taxa()

""" /------------[4]------------ A + | /---------[3]--------- B ---[1]---+ ------------[4]------------- C

labels = ('A', 'B', 'C') dm = [[0. 8. 9.] [8. 0. 7.] [9. 7. 0.]] """

e.g. The following commands (equivalent) get the distance between A and B

dm[0, 1] # 8 dm[labels.index('A'), labels.index('B')] # 8 ```

Normalisation

If the norm argument of dm is set to True, then the data will be normalised by the sum of all edges in the tree.

⏱ Performance

Tests were executed using scripts/performance/Snakefile on an Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz.

For large numbers of taxa it is beneficial to use PhyloDM, however, if you have a small number of taxa in the tree it is beneficial to use DendroPy for the great features it provides.

PhyloDM vs DendroPy resource usage

Owner

Name: Aaron Mussig
Login: aaronmussig
Kind: user
Location: Brisbane, Australia
Company: Australian Centre for Ecogenomics

Twitter: aaronmussig
Repositories: 7
Profile: https://github.com/aaronmussig

Bioinformatics PhD student at the University of Queensland. Python and Rust enthusiast.

Citation (CITATION.cff)

cff-version: 1.2.0
abstract: "Efficient calculation of phylogenetic distance matrices."
message: "If you use this software, please cite it as below."
authors:
- family-names: "Mussig"
  given-names: "Aaron J."
  orcid: "https://orcid.org/0000-0002-9988-0866"
title: "PhyloDM"
version: 3.2.0
doi: 10.5281/zenodo.3998716
url: "https://github.com/aaronmussig/PhyloDM"
date-released: 2024-10-08
keywords:
 - phylogenetic
 - tree
 - "distance matrix"
license: GPL-3.0

GitHub Events

Total

Watch event: 2
Fork event: 1

Last Year

Watch event: 2
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 95
Total Committers: 3
Avg Commits per committer: 31.667
Development Distribution Score (DDS): 0.137

Past Year

Commits: 14
Committers: 2
Avg Commits per committer: 7.0
Development Distribution Score (DDS): 0.214

Top Committers

Name	Email	Commits
Aaron Mussig	a**g@g**m	82
semantic-release-bot	s**t@m**t	11
dependabot[bot]	4****]	2

Committer Domains (Top 20 + Academic)

martynus.net: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 7
Total pull requests: 13
Average time to close issues: 7 months
Average time to close pull requests: about 1 month
Total issue authors: 6
Total pull request authors: 3
Average comments per issue: 2.29
Average comments per pull request: 1.31
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 4

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 1 minute
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

CNwangbin (2)
FinnOD (1)
drdna (1)
jianshu93 (1)
aaronmussig (1)
wanxn518 (1)

Pull Request Authors

aaronmussig (8)
dependabot[bot] (4)
FinnOD (2)

Top Labels

Issue Labels

enhancement (2) help wanted (1) bug (1)

Pull Request Labels

released (6) dependencies (4)

Packages

Total packages: 3
Total downloads:
- pypi 707 last-month
- cargo 11,090 total

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 28
Total maintainers: 2

pypi.org: phylodm

Efficient calculation of phylogenetic distance matrices.

Homepage: https://github.com/aaronmussig/PhyloDM
Documentation: https://github.com/aaronmussig/PhyloDM
License: GPL-3.0
Latest release: 3.2.0
published over 1 year ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 690 Last month

Rankings

Dependent packages count: 10.0%

Stargazers count: 10.2%

Average: 17.4%

Dependent repos count: 21.7%

Downloads: 22.5%

Forks count: 22.6%

Maintainers (1)

aaronmussig

Last synced: 7 months ago

pypi.org: metatree

Visualisation of polyphyletic groups between phylogenetic trees to a reference tree.

Homepage: https://github.com/aaronmussig/metatree
Documentation: https://github.com/aaronmussig/PhyloDM
License: GPL3
Latest release: 0.0.1
published over 5 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 17 Last month

Rankings

Dependent packages count: 10.0%

Stargazers count: 10.3%

Dependent repos count: 21.7%

Forks count: 22.6%

Average: 26.2%

Downloads: 66.3%

Maintainers (1)

aaronmussig

Last synced: 7 months ago

crates.io: phylodm

Efficient calculation of phylogenetic distance matrices.

Documentation: https://docs.rs/phylodm/
License: GPL-3.0
Latest release: 3.2.0
published over 1 year ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 11,090 Total

Rankings

Stargazers count: 18.5%

Dependent repos count: 29.3%

Dependent packages count: 33.8%

Average: 35.6%

Forks count: 37.5%

Downloads: 59.1%

Maintainers (1)

aaronmussig

Last synced: 7 months ago

Dependencies

Cargo.lock cargo

aho-corasick 0.7.18
ansi_term 0.12.1
atty 0.2.14
autocfg 1.1.0
bitflags 1.3.2
cfg-if 1.0.0
clap 2.34.0
convert_case 0.4.0
derive_more 0.99.17
either 1.7.0
env_logger 0.8.4
getopt 1.1.3
getrandom 0.1.16
heck 0.3.3
hermit-abi 0.1.19
humantime 2.1.0
indoc 1.0.6
itertools 0.10.3
lazy_static 1.4.0
libc 0.2.126
light_phylogeny 1.4.5
lock_api 0.4.7
log 0.4.17
matrixmultiply 0.3.2
memchr 2.5.0
ndarray 0.15.4
num-complex 0.4.2
num-integer 0.1.45
num-traits 0.2.15
numpy 0.16.2
once_cell 1.13.0
parking_lot 0.12.1
parking_lot_core 0.9.3
ppv-lite86 0.2.16
proc-macro-error 1.0.4
proc-macro-error-attr 1.0.4
proc-macro2 1.0.40
pyo3 0.16.5
pyo3-build-config 0.16.5
pyo3-ffi 0.16.5
pyo3-macros 0.16.5
pyo3-macros-backend 0.16.5
quote 1.0.20
rand 0.7.3
rand_chacha 0.2.2
rand_core 0.5.1
rand_hc 0.2.0
rand_pcg 0.2.1
random_color 0.5.1
rawpointer 0.2.1
redox_syscall 0.2.13
regex 1.6.0
regex-syntax 0.6.27
roxmltree 0.14.1
rustc_version 0.4.0
scopeguard 1.1.0
semver 1.0.12
smallvec 1.9.0
strsim 0.8.0
structopt 0.3.26
structopt-derive 0.4.18
svg 0.8.2
syn 1.0.98
target-lexicon 0.12.4
termcolor 1.1.3
textwrap 0.11.0
unicode-ident 1.0.2
unicode-segmentation 1.9.0
unicode-width 0.1.9
unindent 0.1.9
vec_map 0.8.2
version_check 0.9.4
wasi 0.9.0+wasi-snapshot-preview1
winapi 0.3.9
winapi-i686-pc-windows-gnu 0.4.0
winapi-util 0.1.5
winapi-x86_64-pc-windows-gnu 0.4.0
windows-sys 0.36.1
windows_aarch64_msvc 0.36.1
windows_i686_gnu 0.36.1
windows_i686_msvc 0.36.1
windows_x86_64_gnu 0.36.1
windows_x86_64_msvc 0.36.1
xmlparser 0.13.3

package-lock.json npm

457 dependencies

package.json npm

@semantic-release/changelog ^6.0.1 development
@semantic-release/commit-analyzer ^9.0.2 development
@semantic-release/exec ^6.0.3 development
@semantic-release/git ^10.0.1 development
@semantic-release/github ^8.0.5 development
@semantic-release/release-notes-generator ^10.0.3 development
semantic-release ^19.0.3 development

setup.py pypi

numpy *

.github/workflows/build-publish.yml actions

actions-rs/cargo v1 composite
actions-rs/toolchain v1 composite
actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-node v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
pypa/cibuildwheel v2.10.0 composite
pypa/gh-action-pypi-publish release/v1 composite

Cargo.toml cargo

pyproject.toml pypi

phylodm

Science Score: 54.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

🌲 PhyloDM

⚙ Installation

PyPI

Conda

🐍 Quick-start

PREPARATION: Create a test tree

1a. From a Newick file

1b. From a DendroPy tree

2. Calculate the PDM

Accessing data

Calculate the PDM

e.g. The following commands (equivalent) get the distance between A and B

Normalisation

⏱ Performance

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: phylodm

Rankings

Maintainers (1)

pypi.org: metatree

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Maintainers (1)

crates.io: phylodm

Rankings

Maintainers (1)

Dependencies