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https://github.com/acg-team/single-char-indel-asr-preserves-long-indels

This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.

https://github.com/acg-team/single-char-indel-asr-preserves-long-indels

Science Score: 26.0%

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Keywords

ancestral-sequence-reconstruction indels
Last synced: 9 months ago · JSON representation

Repository

This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.

Basic Info
  • Host: GitHub
  • Owner: acg-team
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 11.2 MB
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ancestral-sequence-reconstruction indels
Created about 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

readme.md

The Python scripts used for the paper entitled:

Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction

Requirments

For this tutorial, you should already have Python 3.9 or higher, jupyter notebook along with the following libraries:

numpy, ete3, biopython, seaborn, matplotlib, sklearn and pandas

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

Files

  • mammals_01_stat.ipynb contains functions for indel pattern plots for mammalian data.
  • mammals_02_dynamic_of_gaps.ipynb includes functions for calculating dynamic of gap pattern for each mammalian data.
  • mammals_03_indel_length.ipynb includes functions for ploting indel length for mammalian data.
  • simulation_01_acc.ipynb contains functions for computing accuracy of ARPIP inference on simulated data.
  • simulation_02_dynamic_of_gaps.ipynb contains functions for calculating dynamic of gap pattern for each simulated data.
  • simulation_03_stat.ipynb contains functions for indel pattern plots for simulated data.
  • simulation_04_discussion.ipynb contains scripts for the appendix figures.
  • requirements.txt contains library versions of dependencies.

To get the figures in the manuscript all the necessary files and scripts are provided here. Moreover, suplemental data is stored in another repository with this link.

Citation

Please cite:

Gholamhossein Jowkar, Julija Pecerska, Manuel Gil, and Maria Anisimova
Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.
BioRxiv, 2024;
doi:10.1101/2024.03.09.584071

Author

Gholam-Hossein Jowkar E-mail

Owner

  • Name: Applied Computational Genomics Team
  • Login: acg-team
  • Kind: organization
  • Location: Wädenswil, Switzerland

Computational Genomics tools from Maria Anisimova and collaborators

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Dependencies

requirements.txt pypi
  • biopython ==1.79
  • ete3 ==3.1.2
  • matplotlib ==3.7.1
  • numpy ==1.23.3
  • pandas ==1.5.0
  • seaborn =0.13.0
  • sklearn =1.1.3