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Sheng-Long Kan et al.
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Sergei L. Mosyakin et al.
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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian-Jun Jin et al.
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Deise J. P. Goncalves et al.
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PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
Xiao-Jian Qu et al.
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Joseph F. Walker et al.
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Shifu Chen et al.
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Shu-Dong Zhang et al.
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Tao Feng et al.
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Xing-Xing Shen et al.
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Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny
Catarina Rydin et al.
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
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AMAS: a fast tool for alignment manipulation and computing of summary statistics
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Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.
Ryan R. Wick et al.
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Stephen A. Smith et al.
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Miao Sun et al.
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Lam-Tung Nguyen et al.
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Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae
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Alexandros Stamatakis
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Leonidas Salichos et al.
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Norman J. Wickett et al.
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Bernhard Misof et al.
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Yang Liu et al.
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Shannon C. K. Straub et al.
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Daniel B. Sloan
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Ultrafast Approximation for Phylogenetic Bootstrap
Bui Quang Minh et al.
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Matthew Kearse et al.
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Mats Topel et al.
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The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell
Thomas Junier et al.
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A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): Implications for its geographic origin, phylogeography and generic circumscription
Christoph Dobes et al.
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Michael J. Moore et al.
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Stephane Guindon et al.
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
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James H. Degnan et al.
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Robert K. Jansen et al.
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David E. McCauley et al.
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Probabilistic analysis indicates discordant gene trees in chloroplast evolution
C Vogl et al.
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Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants
KL Adams et al.
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Paternal inheritance of chloroplast DNA in interspecific hybrids in the genus Larrea (Zygophyllaceae)
TW Yang et al.
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Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes in Silene vulgaris
MS Olson et al.
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