SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
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[1] Hannes Hettling,et al. phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R , 2018, Life.
[2] Andy Purvis,et al. phyloGenerator: an automated phylogeny generation tool for ecologists , 2013 .
[3] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[4] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[5] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[6] V. Ranwez,et al. MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons , 2018, Molecular biology and evolution.
[7] Uetz Peter,et al. The Reptile Database , 1995 .
[8] Eduard Szöcs,et al. taxize: taxonomic search and retrieval in R , 2013, F1000Research.
[9] R. T. Brumfield,et al. Applications of next-generation sequencing to phylogeography and phylogenetics. , 2013, Molecular phylogenetics and evolution.
[10] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[11] Matthieu Muffato,et al. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference , 2015, Systematic biology.
[12] J. Gatesy,et al. The supermatrix approach to systematics. , 2007, Trends in ecology & evolution.
[13] J. Hancock,et al. Ethylene-induced stomatal closure in Arabidopsis occurs via AtrbohF-mediated hydrogen peroxide synthesis. , 2006, The Plant journal : for cell and molecular biology.
[14] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[15] Brant C. Faircloth,et al. PHYLUCE is a software package for the analysis of conserved genomic loci , 2015, bioRxiv.
[16] Tsippi Iny Stein,et al. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses , 2016, Current protocols in bioinformatics.
[17] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[18] Tandy J. Warnow,et al. Ultra-large alignments using phylogeny-aware profiles , 2015, Genome Biology.
[19] Bin Ma,et al. PatternHunter: faster and more sensitive homology search , 2002, Bioinform..
[20] M. Donoghue,et al. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches , 2009, BMC Evolutionary Biology.
[21] Stephen A. Smith,et al. PyPHLAWD: A python tool for phylogenetic dataset construction , 2018, Methods in Ecology and Evolution.
[22] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[23] William A. Freyman. SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage , 2015, Evolutionary bioinformatics online.
[24] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[25] R. Henrik Nilsson,et al. Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa , 2016, Systematic biology.
[26] Serita M. Nelesen,et al. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. , 2012, Systematic biology.
[27] Tandy J. Warnow,et al. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences , 2015, J. Comput. Biol..
[28] Duhong Chen,et al. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. , 2008, Systematic biology.
[29] Anne Thessen,et al. Challenges with using names to link digital biodiversity information , 2016, Biodiversity data journal.
[30] B. Carstens,et al. The evolution of phylogeographic data sets , 2015, Molecular ecology.