Journal ArticleDOI
MITOS: Improved de novo metazoan mitochondrial genome annotation
Matthias Bernt,Alexander Donath,Frank Jühling,Frank Jühling,Fabian Externbrink,Catherine Florentz,Guido Fritzsch,Joern Pütz,Martin Middendorf,Peter F. Stadler +9 more
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TLDR
The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-11-01. It has received 3323 citations till now. The article focuses on the topics: RefSeq.read more
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The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods.
TL;DR: The complete mitochondrial (mt) genome sequence of the South China deep‐sea giant isopod Bathynomus sp.
Journal ArticleDOI
Mitochondrial phylogenomics, the origin of swallowtail butterflies, and the impact of the number of clocks in Bayesian molecular dating
Fabien L. Condamine,Fabien L. Condamine,Benoit Nabholz,Anne-Laure Clamens,Anne-Laure Clamens,Julian R. Dupuis,Felix A. H. Sperling +6 more
TL;DR: A mitogenomic, time‐calibrated phylogeny for all swallowtail genera is presented, confirming that Baroniinae is sister to Parnassiinae + Papilioninae, both recovered as monophyletic and laying the foundations for classification at tribe and genus level.
Journal ArticleDOI
The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications.
TL;DR: The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results, both supporting the monophyly of all stonefly families and the two infraorders, Systellognatha and Euholognatha.
Journal ArticleDOI
New insights into the phylogenetics and population structure of the prairie falcon ( Falco mexicanus )
Jacqueline M. Doyle,Jacqueline M. Doyle,Douglas A. Bell,Peter H. Bloom,Gavin Emmons,Amy Fesnock,Todd E. Katzner,Larry LaPre,Kolbe Leonard,Phillip SanMiguel,Rick Westerman,J. Andrew DeWoody +11 more
TL;DR: California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.
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Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota
Luis Javier Galindo,Purificación López-García,Guifré Torruella,Sergey Karpov,Sergey Karpov,David Moreira +5 more
TL;DR: In this article, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis were sequenced to assess their phylogenetic position and evolution.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
Journal ArticleDOI
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock,Tiago Antao,Jeffrey T. Chang,Brad Chapman,Cymon J. Cox,Andrew Dalke,Iddo Friedberg,Thomas Hamelryck,Frank Kauff,Bartosz Wilczyński,Michiel J. L. de Hoon +10 more
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Journal ArticleDOI
Automatic annotation of organellar genomes with DOGMA
TL;DR: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
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