Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 69, Issue 2, Pages 320-327Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2012.09.019
Keywords
Bioinformatics; Mitochondria; Genome rearrangements; Substitution models; Gene annotation
Funding
- German Research Foundation (DFG) through the Project Deep Metazoan Phylogeny within SPP 1174 [STA 850/3-2, STA 850/2]
- Marie-Curie/Province of Trento (COFOUND) fellowship
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In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models. We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity. (C) 2012 Elsevier Inc. All rights reserved.
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