https://github.com/acg-team/indelviewer
Indel viewer software for ARPIP
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary
Keywords
Repository
Indel viewer software for ARPIP
Basic Info
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
ARPIP's Indel Visualizer
This repository contains the implementation of the arpip indel viewer which help the user to visualize the indel points
inferred by ARPIP in the phylogenetic tree.
Getting Started
Before installation make sure that you have the Python version 3.8 or higher installed on your system. Need help?
Installation
To install the package you can simply download the repository and run the following command in the root directory.
Install the dependencies using this command:
console
pip3 install -r requirements.txt
Usage
The user can run the visualizer using the command line. For running the application use this command:
console
python ./main.py ./input.txt
To print a single site tree with indel points use this command:
console
python ./_cli.py --single-result 102 ./input.txt
for print all site tree with indel points use this command:
console
python ./_cli.py ./input.txt
for help use this command:
console
python ./_cli.py —help
Articles
- For more information on IndelPoints algorithm, see Jowkar et al.'s 2022 paper which can be located here.
Contributing
If you want to contribute to this repo simply submit a pull request!
Author
Gholam-Hossein Jowkar E-mail
Owner
- Name: Applied Computational Genomics Team
- Login: acg-team
- Kind: organization
- Location: Wädenswil, Switzerland
- Website: https://www.zhaw.ch/de/lsfm/institute-zentren/ias/forschung/computational-genomics/
- Repositories: 29
- Profile: https://github.com/acg-team
Computational Genomics tools from Maria Anisimova and collaborators
GitHub Events
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Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gholamhossein Jowkar | g****k@y****k | 49 |
| Gholamhossein Jowkar | 6****r | 1 |
Committer Domains (Top 20 + Academic)
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Last synced: about 2 years ago
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- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
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- Bot pull requests: 0
Past Year
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- Average time to close issues: N/A
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Dependencies
- IPython ==8.6.0
- biopython ==1.79
- bokeh ==2.4.3
- ete3 ==3.1.2
- matplotlib ==3.7.1
- numpy ==1.23.3
- pandas ==1.5.0
- panel ==0.14.1