Related Experiment Video
Updated: Jun 22, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutiérrez1, José M Silla-Martínez, Toni Gabaldón
1Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain.
Bioinformatics (Oxford, England)
|June 10, 2009
Summary
trimAl is a new automated tool for alignment trimming, improving phylogenetic analysis quality. It efficiently removes poorly aligned regions from large datasets, optimizing signal-to-noise ratio.
Area of Science:
- Bioinformatics
- Computational Biology
- Phylogenetics
Background:
- Multiple sequence alignments are crucial for bioinformatics analyses.
- Poorly aligned regions can compromise the quality of downstream analyses.
- Trimming alignments enhances the reliability of phylogenetic studies.
Purpose of the Study:
- To introduce trimAl, an automated tool for alignment trimming.
- To provide a solution for large-scale phylogenetic analyses involving thousands of alignments.
- To improve the efficiency and accuracy of phylogenetic analyses through automated alignment curation.
Main Methods:
- trimAl utilizes several parameters for selecting reliable alignment positions.
- Parameters include gap proportion, amino acid similarity, and cross-alignment consistency.
- The tool can automatically select optimal parameters for each alignment.
Main Results:
- trimAl facilitates automated alignment trimming for large datasets.
- It enhances the quality of phylogenetic analyses by removing unreliable regions.
- The tool optimizes the signal-to-noise ratio in alignments.
Conclusions:
- trimAl is a powerful and versatile tool for automated alignment trimming.
- It is particularly well-suited for large-scale phylogenetic analyses.
- The software improves the accuracy and efficiency of bioinformatics workflows.
More Related Videos
10:23A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
10:40Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
03:21Phylogenetic Trees
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
03:21Phylogenetic Trees
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
01:23Phylogeny
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.