Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

Abstract Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated...

Full description

Saved in:
Bibliographic Details
Published in:Systematic biology Vol. 64; no. 5; pp. 778 - 791
Main Authors: Tan, Ge, Muffato, Matthieu, Ledergerber, Christian, Herrero, Javier, Goldman, Nick, Gil, Manuel, Dessimoz, Christophe
Format: Journal Article
Language:English
Published: England Oxford University Press 01.09.2015
Subjects:
Algorithms
Classification - methods
Genome - genetics
Phylogeny
Reproducibility of Results
Sequence Alignment
phylogenetic inference
alignment trimming
alignment filtering
molecular phylogeny
multiple sequence alignment
phylogeny
phylogenetics
ISSN:1063-5157, 1076-836X, 1076-836X
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1063-5157
1076-836X
1076-836X
DOI:10.1093/sysbio/syv033