Nemu-pipeline

This repository contains the pipeline for neutral mutational spectra evaluation based on evolutionary data and materials for the publication titled "NeMu: A Comprehensive Pipeline for Accurate Reconstruction of Neutral Mutation Spectra from Evolutionary Data" by Efimenko B. et al.

Webserver

Enjoy the pipeline using our user-friendly webserver!

Check Wiki to read how to use the pipeline

Repository details

• ./pipeline/ directory contains *.nf files (Nextflow) with 2 versions of the pipeline: for single-protein and multiple-nucleotide inputs
• ./singularity/ - definition files for the container used to store all dependencies
• ./data/ - several intermediate files from analyses, example inputs, full example run and supplementary data for the article
• ./figures/ - figures from all performed analyses and comparisons, pipeline schemes, etc.
• ./notebooks/ - all performed analyses on python
• ./scripts/ - all used scripts for specific data processing during analyses and scripts, used in the NeMu pipeline
• ./docs/ - notes for used tools

Each main directory contains readme file with detailed information.

Dependencies

Singularity container

The pipeline relies on a diverse set of dependencies. To simplify execution, ensure compatibility across different operating systems, all these dependencies have been packaged within a Singularity container. We used Singularity 3.10.2.

Used software

Here listed all dependencies used in the NeMu pipeline during mutatoinal spectra calculations:

• Linux (e.g. Ubuntu)
• Nextflow 22.10.7
• Python 3.8.12
• Perl v5.16.3
• R 3.6.0

1. BLAST+ 2.13.0 for tblast search in nucleotide sequences databases;
2. Mview 1.67 for blast-report reformatting;
3. Custom Perl scripts for sequences extraction and filtration;
4. MACSE v2.06 and MAFFT 7.505 for nucleotide sequences alignment considering codon structure;
5. IQ-TREE2 2.2.0 for tree building, ancestral reconstruction and site rates estimation;
6. TreeShrink 1.3.9 for outlier branch filtration;
7. Newick-tools 1.6 for tree rerooting and other tree processing;
8. Pymutspec 0.0.8 Python package that we developed for mutation extraction and spectrum calculation.
9. Pyvolve 1.1.0 (modified) for neutral evolution simutation using MutSel models

How to cite?

Bogdan Efimenko, Konstantin Popadin, Konstantin Gunbin, NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data, Nucleic Acids Research, Volume 52, Issue W1, 5 July 2024, Pages W108–W115, https://doi.org/10.1093/nar/gkae438