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wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

https://github.com/sunpengchuan/wgdi

Science Score: 13.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (13.8%) to scientific vocabulary

Keywords

ancestral-chromosomal-karyotype bioinformatics collinearity polyploidy
Last synced: 6 months ago · JSON representation

Repository

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Basic Info
Statistics
  • Stars: 144
  • Watchers: 2
  • Forks: 24
  • Open Issues: 11
  • Releases: 0
Topics
ancestral-chromosomal-karyotype bioinformatics collinearity polyploidy
Created over 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

WGDI

Latest PyPI version Downloads install with bioconda

| | | | --- | --- | | Author | Pengchuan Sun (sunpengchuan) | | Email | sunpengchuan@gmail.com | | License | BSD |

Description

WGDI (Whole-Genome Duplication Integrated analysis) is a Python-based command-line tool designed to simplify the analysis of whole-genome duplications (WGD) and cross-species genome alignments. It offers three main workflows that enhance the detection and study of WGD events:

Key Features

1. Polyploid Inference

  • Identifies and confirms polyploid events with high accuracy.

2. Genomic Homology Inference

  • Traces the evolutionary history of duplicated regions across species, with a focus on distinguishing subgenomes.

3. Ancestral Karyotyping

  • Reconstructs protochromosomes and traces common chromosomal rearrangements to understand chromosome evolution.

Installation

Python package and command line interface (IDLE) for the analysis of whole genome duplications (WGDI). WGDI can be deployed in Windows, Linux, and Mac OS operating systems and can be installed via pip and conda.

Bioconda

conda install -c bioconda wgdi

Pypi

pip3 install wgdi

Documentation for installation along with a user tutorial, a default parameter file, and test data are provided. please consult the docs at http://wgdi.readthedocs.io/en/latest/.

Tips

Here are some videos with simple examples of WGDI.

WGDI的简单使用（一） or https://youtu.be/k-S6FVcBIQw
WGDI的简单使用（二） or https://youtu.be/QiZYFYGclyE

chatting group QQ : 966612552

Citating WGDI

If you use wgdi in your work, please cite:

Sun P., Jiao B., Yang Y., Shan L., Li T., Li X., Xi Z., Wang X., and Liu J. (2022). WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.10.018.

News

0.74

  • Improved the the fusion positions dataset (-fpd).
  • Fixed some issues (-pc).

0.7.1

  • Added extract the fusion positions dataset (-fpd).
  • Added determine whether these fusion events occur in other genomes (-fd).
  • Improved the karyotype_mapping (-km) effect.
  • Fixed the problem caused by the Python version, now it is compatible with version 3.12.

0.6.5

  • Fixed some issues (-sf).
  • Added new tips to avoid some errors.

0.6.4

  • Fixed the problem caused by the Python version, now it is compatible with version 3.11.3.

0.6.3

  • Fixed some issues (-ks, -sf).

0.6.2

  • Added find shared fusions between species (-sf).

0.6.1

  • Fixed issue with alignment (-a). Only version 0.6.0 has this bug.

0.6.0

  • Fixed issue with improved collinearity (-icl).
  • Added a parameter 'tandem_ratio' to blockinfo (-bi).

0.5.9

  • Update the improved collinearity (-icl). Faster than before, but lower than MCscanX, JCVI.
  • Fixed issue with ancestral karyotype repertoire (-akr).

0.5.8

  • Fixed issue with gene names (-ks).

0.5.7

  • Fixed issue with chromosome order (-ak).
  • Fixed issue with gene names (-ks). This version is not fixed, please install the latest version.

0.5.5 and 0.5.6

  • Add ancestral karyotype (-ak)
  • Add ancestral karyotype repertoire (-akr)

0.5.4

  • Improved the karyotype_mapping (-km) effect.
  • little change (-at).

0.5.3

  • Fixed legend issue with (-kf).
  • Fixed calculate Ks issue with (-ks).
  • Improved the karyotype_mapping (-km) effect.
  • Improved the alignmenttrees (-at) effect.

0.5.2

  • Fixed some bugs.

0.5.1

  • Fixed the error of the command (-conf).
  • Improved the karyotype_mapping (-km) effect.
  • Added the available data set of alignmenttree (-at). Low copy data set (for example, single-copy_groups.tsv of sonicparanoid2 software).

0.4.9

  • The latest version adds karyotype_mapping (-km) and karyotype (-k) display.
  • The latest version changes the calculation of extracting pvalue from collinearity (-icl), making this parameter more sensitive. Therefore, it is recommended to set to 0.2 instead of 0.05.
  • The latest version has also changed the drawing display of ksfigure (-kf) to make it more beautiful.

Owner

  • Name: sunpengchuan
  • Login: SunPengChuan
  • Kind: user
  • Location: Chengdu, 610065, China.
  • Company: Sichuan University

Bioinformatics data analysis

GitHub Events

Total
  • Issues event: 12
  • Watch event: 19
  • Issue comment event: 20
  • Push event: 6
  • Pull request event: 1
  • Fork event: 3
Last Year
  • Issues event: 12
  • Watch event: 19
  • Issue comment event: 20
  • Push event: 6
  • Pull request event: 1
  • Fork event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 68
  • Total Committers: 2
  • Avg Commits per committer: 34.0
  • Development Distribution Score (DDS): 0.235
Top Committers
Name Email Commits
sunpengchuan s****n@g****m 52
sunpc 1****2@q****m 16
Committer Domains (Top 20 + Academic)
qq.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 57
  • Total pull requests: 3
  • Average time to close issues: 27 days
  • Average time to close pull requests: about 15 hours
  • Total issue authors: 35
  • Total pull request authors: 2
  • Average comments per issue: 3.95
  • Average comments per pull request: 0.33
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 1
  • Average time to close issues: 2 days
  • Average time to close pull requests: N/A
  • Issue authors: 6
  • Pull request authors: 1
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • tinyfallen (7)
  • ardy20 (6)
  • Wenwen012345 (4)
  • sajjadasaf (3)
  • amvarani (3)
  • Jiangjiangzhang6 (2)
  • kuangzhuoran (2)
  • xiekunwhy (2)
  • cfz1998 (2)
  • bitahu (1)
  • pxxiao-hz (1)
  • zhangzk-jiangsu-nanjing (1)
  • bebestcf (1)
  • mamtamasand (1)
  • 000001236 (1)
Pull Request Authors
  • starskyzheng (2)
  • yukaiquan (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 128 last-month
  • Total docker downloads: 100
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 31
  • Total maintainers: 1
pypi.org: wgdi

A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

  • Versions: 31
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 128 Last month
  • Docker Downloads: 100
Rankings
Docker downloads count: 2.3%
Stargazers count: 7.4%
Forks count: 8.6%
Dependent packages count: 10.0%
Average: 11.2%
Downloads: 17.1%
Dependent repos count: 21.7%
Maintainers (1)
sunpc
Last synced: 6 months ago