Journal ArticleDOI
Applications of next-generation sequencing to phylogeography and phylogenetics
TLDR
In this article, the authors outline some of the major obstacles specific to the application of NGS to phylogeography and phylogenetics, including the focus on non-model organisms, the necessity of obtaining orthologous loci in a cost-effective manner, and the predominate use of gene trees in these fields.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-02-01. It has received 586 citations till now. The article focuses on the topics: Phylogenomics.read more
Citations
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DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.
Julio Rozas,Albert Ferrer-Mata,Juan Carlos Sánchez-DelBarrio,Sara Guirao-Rico,Pablo Librado,Pablo Librado,Sebastian E. Ramos-Onsins,Alejandro Sánchez-Gracia +7 more
TL;DR: The DNA Sequence Polymorphism (DnaSP) software as mentioned in this paper is a popular tool for performing exhaustive population genetic analyses on multiple sequence alignments, such as single and multi-locus coalescent simulations under a wide range of demographic scenarios.
Journal ArticleDOI
Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
TL;DR: The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Journal ArticleDOI
How to fail at species delimitation.
TL;DR: Researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Journal ArticleDOI
High-Throughput Genomic Data in Systematics and Phylogenetics
TL;DR: This review presents recent advances in laboratory methods for collection of high-throughput phylogenetic data and challenges and constraints for phylogenetic analysis of these data, and offers recommendations for the most promising protocols and data-analysis workflows currently available.
Journal ArticleDOI
AMAS: a fast tool for alignment manipulation and computing of summary statistics.
TL;DR: AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package, works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics.
References
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Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
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AFLP: a new technique for DNA fingerprinting.
Pieter Vos,René Cornelis Josephus Hogers,Marjo Bleeker,Martin Reijans,Theo van de Lee,Miranda Hornes,Adrie Friters,Jerina Pot,Johan Paleman,Martin Kuiper,Marc Zabeau +10 more
TL;DR: The AFLP technique provides a novel and very powerful DNA fingerprinting technique for DNAs of any origin or complexity that allows the specific co-amplification of high numbers of restriction fragments.