相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
Tobias Andermann et al.
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SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
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Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci
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Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)
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Erin K. Molloy et al.
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The performance of coalescent-based species tree estimation methods under models of missing data
Michael Nute et al.
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Estimating Improved Partitioning Schemes for Ultraconserved Elements
Victor A. Tagliacollo et al.
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Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci
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MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)
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SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Tobias Andermann et al.
PEERJ (2018)
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
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LIFE-BASEL (2018)
Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
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MOLECULAR PHYLOGENETICS AND EVOLUTION (2017)
Phylotranscriptomic consolidation of the jawed vertebrate timetree
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NATURE ECOLOGY & EVOLUTION (2017)
Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families
Jeffrey W. Streicher et al.
BIOLOGY LETTERS (2017)
PHYLUCE is a software package for the analysis of conserved genomic loci
Brant C. Faircloth
BIOINFORMATICS (2016)
Multiple sequence alignment modeling: methods and applications
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BRIEFINGS IN BIOINFORMATICS (2016)
The Impact of Missing Data on Species Tree Estimation
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MOLECULAR BIOLOGY AND EVOLUTION (2016)
Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status
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BIOLOGICAL CONSERVATION (2016)
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Adam D. Leache et al.
BMC EVOLUTIONARY BIOLOGY (2016)
Scaling statistical multiple sequence alignment to large datasets
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BMC GENOMICS (2016)
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
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MOLECULAR BIOLOGY AND EVOLUTION (2016)
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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MOLECULAR BIOLOGY AND EVOLUTION (2016)
An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
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MOLECULAR ECOLOGY RESOURCES (2016)
Phylogenomic analyses reveal novel relationships among snake families
Jeffrey W. Streicher et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2016)
Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species
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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).
Charles W. Linkem et al.
SYSTEMATIC BIOLOGY (2016)
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
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SYSTEMATIC BIOLOGY (2016)
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
Siavash Mirarab et al.
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Phylogenomics of Horned Lizards (Genus: Phrynosoma) Using Targeted Sequence Capture Data
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SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage
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PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
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Ultra-large alignments using phylogeny-aware profiles
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Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa
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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
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BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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BIOINFORMATICS (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds
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SCIENCE (2014)
Naive binning improves phylogenomic analyses
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BIOINFORMATICS (2013)
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
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MOLECULAR BIOLOGY AND EVOLUTION (2013)
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Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
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BIOLOGY LETTERS (2012)
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
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Accounting For Alignment Uncertainty in Phylogenomics
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SYSTEMATIC BIOLOGY (2012)
Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation
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MOLECULAR PHYLOGENETICS AND EVOLUTION (2011)
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
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MOLECULAR SYSTEMS BIOLOGY (2011)
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PLOS ONE (2011)
The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
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SYSTEMATIC BIOLOGY (2011)
Estimating Species Trees from Unrooted Gene Trees
Liang Liu et al.
SYSTEMATIC BIOLOGY (2011)
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
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BMC EVOLUTIONARY BIOLOGY (2010)
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
Carsten Kemena et al.
BIOINFORMATICS (2009)
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
BIOINFORMATICS (2009)
Noisy:: Identification of problematic columns in multiple sequence alignments
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ALGORITHMS FOR MOLECULAR BIOLOGY (2008)
Branch lengths, support, and congruence: Testing the phylogenomic approach with 20 nuclear loci in snakes
John J. Wiens et al.
SYSTEMATIC BIOLOGY (2008)
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
Gerard Talavera et al.
SYSTEMATIC BIOLOGY (2007)
Nematode small subunit phylogeny correlates with alignment parameters
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SYSTEMATIC BIOLOGY (2006)
Multiple sequence alignment accuracy and phylogenetic inference
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SYSTEMATIC BIOLOGY (2006)
Multiple sequence alignment
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The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes
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COMPTES RENDUS BIOLOGIES (2005)
MAFFT version 5: improvement in accuracy of multiple sequence alignment
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NUCLEIC ACIDS RESEARCH (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
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NUCLEIC ACIDS RESEARCH (2004)
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SCIENCE (2004)
Molecular phylogenetics of Squamata: The position of snakes, Amphisbaenians, and Dibamids, and the root of the Squamate tree
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
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NUCLEIC ACIDS RESEARCH (2002)
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GENOME RESEARCH (2002)
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MOLECULAR BIOLOGY AND EVOLUTION (2000)
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