Phylogenomics from low‐coverage whole‐genome sequencing

[1]  J. Good,et al.  Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales , 2012, BMC Genomics.

[2]  Toni Gabaldón,et al.  Redundans: an assembly pipeline for highly heterozygous genomes , 2015, Nucleic acids research.

[3]  Evgeny M. Zdobnov,et al.  OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs , 2016, Nucleic Acids Res..

[4]  R. T. Brumfield,et al.  Applications of next-generation sequencing to phylogeography and phylogenetics. , 2013, Molecular phylogenetics and evolution.

[5]  A. von Haeseler,et al.  UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.

[6]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  T. Sicheritz-Pontén,et al.  Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data , 2017, BMC Bioinformatics.

[8]  Variant calling in low-coverage whole genome sequencing of a Native American population sample , 2014, BMC Genomics.

[9]  J. Townsend,et al.  A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2015, Nature.

[10]  Leping Li,et al.  ART: a next-generation sequencing read simulator , 2012, Bioinform..

[11]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[12]  Robert M. Waterhouse,et al.  Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders , 2017, Genome biology and evolution.

[13]  P. J. Maughan,et al.  Targeted enrichment strategies for next-generation plant biology. , 2012, American journal of botany.

[14]  Antonis Rokas,et al.  Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data , 2016, G3: Genes, Genomes, Genetics.

[15]  Chao Zhang,et al.  ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.

[16]  B. Langmead,et al.  Lighter: fast and memory-efficient sequencing error correction without counting , 2014, Genome Biology.

[17]  Thomas K. F. Wong,et al.  Phylogenomics resolves the timing and pattern of insect evolution , 2014, Science.

[18]  Paul Medvedev,et al.  Compacting de Bruijn graphs from sequencing data quickly and in low memory , 2016, Bioinform..

[19]  Travis C Glenn,et al.  Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.

[20]  Md. Shamsuzzoha Bayzid,et al.  Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.

[21]  Adrian W. Briggs,et al.  Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes , 2009, Science.

[22]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[23]  Brant C. Faircloth,et al.  PHYLUCE is a software package for the analysis of conserved genomic loci , 2015, bioRxiv.

[24]  Kevin P. Johnson,et al.  aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data , 2015, BMC Bioinformatics.

[25]  Lars Arvestad,et al.  BESST - Efficient scaffolding of large fragmented assemblies , 2014, BMC Bioinformatics.

[26]  L. Bachmann,et al.  Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach , 2013, Nucleic acids research.

[27]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[28]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[29]  Robert M. Waterhouse,et al.  BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.

[30]  J. Good,et al.  Targeted capture in evolutionary and ecological genomics , 2016, Molecular ecology.

[31]  Navin Rustagi,et al.  Extremely low-coverage whole genome sequencing in South Asians captures population genomics information , 2017, BMC Genomics.

[32]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[33]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[34]  Todd H. Oakley,et al.  Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny. , 2013, Molecular biology and evolution.

[35]  A. Ives,et al.  Reconstructing phylogeny from reduced‐representation genome sequencing data without assembly or alignment , 2018, Molecular ecology resources.

[36]  R. Lanfear,et al.  Selecting optimal partitioning schemes for phylogenomic datasets , 2014, BMC Evolutionary Biology.

[37]  Rayan Chikhi,et al.  Space-efficient and exact de Bruijn graph representation based on a Bloom filter , 2012, Algorithms for Molecular Biology.

[38]  Roger S Lasken,et al.  Genomic DNA amplification by the multiple displacement amplification (MDA) method. , 2009, Biochemical Society transactions.

[39]  M. Reemer,et al.  Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae) , 2016, BMC Evolutionary Biology.

[40]  Jay Shendure,et al.  Methods for genomic partitioning. , 2009, Annual review of genomics and human genetics.

[41]  Kevin P. Johnson,et al.  Phylogenomics from Whole Genome Sequences Using aTRAM , 2017, Systematic biology.

[42]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[43]  A. Lemmon,et al.  High-Throughput Genomic Data in Systematics and Phylogenetics , 2013 .

[44]  Siavash Mirarab,et al.  Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies , 2016, Molecular biology and evolution.

[45]  P. Kück,et al.  FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies , 2014, Frontiers in Zoology.

[46]  Gonzalo Giribet,et al.  Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life , 2018, Current Biology.

[47]  B. Faircloth,et al.  Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera , 2017 .

[48]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[49]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[50]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[51]  Mihai Pop,et al.  Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies , 2011, BMC Bioinformatics.

[52]  A. Lemmon,et al.  Anchored hybrid enrichment for massively high-throughput phylogenomics. , 2012, Systematic biology.

[53]  B. Faircloth Identifying conserved genomic elements and designing universal bait sets to enrich them , 2017 .

[54]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[55]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[56]  Martin Kollmar,et al.  A novel hybrid gene prediction method employing protein multiple sequence alignments , 2011, Bioinform..