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Updated: Apr 20, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Indel reliability in indel-based phylogenetic inference.

Haim Ashkenazy¹, Ofir Cohen², Tal Pupko³

¹Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.

Genome Biology and Evolution

|November 21, 2014

Summary

This summary is machine-generated.

Phylogenetic reconstruction using insertions and deletions (indels) can be improved by filtering unreliable data. This study introduces a method to score indel reliability, enhancing evolutionary tree accuracy.

Keywords:

alignment reliability indel analysis multiple sequence alignment phylogeny

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Area of Science:

Evolutionary biology
Bioinformatics
Computational phylogenetics

Background:

Insertion/deletion (indel) events are often assumed to be homoplasy-free in phylogenetic inference.
Indels have resolved complex evolutionary relationships but are sensitive to alignment errors.
Current indel-based phylogenetic methods may be inaccurate due to reliance on all inferred indel data.

Purpose of the Study:

To develop a method for quantifying the reliability of indel characters for phylogenetic reconstruction.
To improve the accuracy of phylogenetic trees inferred using indel data.
To assess the impact of filtering and weighting indels based on reliability.

Main Methods:

Quantified indel reliability by measuring their frequency across alternative multiple sequence alignments.
Developed a method assuming consistently present indels across alignments are more reliable.
Applied filtering and weighting strategies using reliability scores to simulated and empirical data.

Main Results:

A novel method was developed to score indel reliability.
Filtering and weighting indels by reliability scores significantly improved phylogenetic reconstruction accuracy.
The approach demonstrated effectiveness on both simulated and real-world biological data.

Conclusions:

Indel character reliability is a crucial factor for accurate phylogenetic inference.
The developed method enhances the utility of indels in resolving evolutionary histories.
This approach offers a more robust way to utilize indel data in phylogenetics.