https://github.com/KatyBrown/CIAlign

https://github.com/KatyBrown/CIAlign

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/KatyBrown/CIAlign
• Owner: KatyBrown
• License: mit
• Created: 2019-04-04T16:22:17.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-05-22T15:22:53.000Z (6 months ago)
• Last Synced: 2024-05-22T18:28:39.393Z (6 months ago)
• Language: Python
• Size: 63.4 MB
• Stars: 103
• Watchers: 4
• Forks: 8
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• Awesome-LatchBio - CIAlign

README

        
![CI](https://github.com/KatyBrown/CIAlign/actions/workflows/main.yml/badge.svg)

# CIAlign

CIAlign documentation is now available via [ReadTheDocs](https://cialign.readthedocs.io/en/latest/)

## Installation

**Requirements**

* python >= 3.6

* matplotlib >= 2.1.1

* numpy >= 1.16.3

* scipy >= 1.3.0

The easiest way to install CIAlign is using conda or pip3.

**Conda**

`conda install -c bioconda cialign`

[link](https://anaconda.org/bioconda/cialign)

**pip3**

`pip3 install cialign`

[link](https://pypi.org/project/cialign/)

**Download**

The current release of CIAlign can also be downloaded directly using [this link](https://github.com/KatyBrown/CIAlign/releases/latest),

If you download the package directly, you will also need to add the CIAlign directory to your PATH environment variable as described [here](https://gist.github.com/nex3/c395b2f8fd4b02068be37c961301caa7)

## Summary

CIAlign allows the user to:

**Clean**

* Remove sources of noise from an MSA 

  * Remove sequences above a threshold level percentage of divergence from the majority.

  * Remove insertions which are not present in the majority of sequences.

  * Crop poorly aligned  sequence ends.

  * Remove short sequences below a threshold number of bases or amino acids.

  * Remove columns containing only gaps.

  * Remove either end of an alignment where columns don't meet a minimum identity threshold and coverage level.

**Visualise**

* Visualise alignments.

  * Generate image files summarising the alignment.

  * Label these images to show how CIAlign has affected the alignment.

  * Draw sequence logos

  * Plot alignment statistics - visualise coverage and conservation at each position in the alignment.

**Interpret**

* Generate consensus sequences.

* Generate position frequency, position probability and position weight matrices

* Format these matrices to be used as input for the BLAMM and MEME motif analysis tools.

* Generate a similarity matrix showing the percentage identity between each sequence pair.

  

**Edit**

* Extract a section of the alignment.

* Unalign the alignment.

* Replace U with T, or T with U in a nucleotide alignment.

CIAlign is designed to be highly customisable, allowing users to specify exactly which functions to run and which settings to use.

It is also transparent, generating a clear log file and alignment markup showing exactly how the alignment has changed and what has been removed by which function.

## Citation

If you found CIAlign useful, please cite: 

Tumescheit C, Firth AE, Brown K. 2022. CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PeerJ 10:e12983 https://doi.org/10.7717/peerj.12983

## Mailing List

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