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Related Experiment Video

Updated: Dec 30, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Processing and Analyzing Multiple Genomes Alignments with MafFilter.

Julien Y Dutheil¹

¹Department of Evolutionary Genetics, Max Planck Institute of Evolutionary Biology, Plön, Germany. dutheil@evolbio.mpg.de.

Methods in Molecular Biology (Clifton, N.J.)

|January 25, 2020

Summary

This summary is machine-generated.

MafFilter is a new tool for processing genome alignments, enabling efficient population genomics analyses. It helps researchers study nucleotide diversity and structural variations across genomes.

Keywords:

Alignment post-processing Multiple alignment format Multiple genome alignment Quality filtering Synteny

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Genomics
Bioinformatics

Background:

Phylogenomics and population genomics are converging due to increased genome sequence availability.
Population genomics traditionally analyzes variants, while phylogenomics uses genome alignments, which are increasingly relevant for population studies.

Purpose of the Study:

Introduce MafFilter, a command-line program for processing Multiple Alignment Format (MAF) genome alignments.
Demonstrate MafFilter's utility in creating reproducible analysis pipelines and performing population genomic analyses.

Main Methods:

Developed MafFilter, a command-line tool for processing MAF files.
Utilized publicly available datasets for demonstration.
Applied MafFilter to quality assurance and downstream analyses.

Main Results:

MafFilter facilitates the development of efficient and reproducible analysis pipelines.
The tool enables both basic and advanced population genomic analyses.
Demonstrated inference of nucleotide diversity patterns along genomes using MafFilter.

Conclusions:

MafFilter is a valuable tool for researchers integrating phylogenomic and population genomic approaches.
It enhances the ability to analyze structural variation and nucleotide diversity from genome alignments.
Promotes reproducible and quality-assured genomic data analysis.