RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Ultrafast approximation for phylogenetic bootstrap.
#Geneious prime software software
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
The complete chloroplast genome of Dendrobium harveyanum (Orchidaceae). Geneious Prime is the world’s leading bioinformatics software platform for molecular biology and sequence analysis. Huang ZC, Pan YY, Chen GZ, Chen LJ, Wu XY, Huang J.A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Louis (MO): Missouri Botanical Garden Press p. Chen SC, Liu ZJ, Zhu GH, Lang KY, Ji ZH, Luo YB, Jin XH, Cribb PJ, Wood JJ, Gale SW, et al.exile with 88% bootstrap values ( Figure 1). Then, the phylogenetic tree was constructed using RAxML (Stamatakis 2014) with 1000 ultrafast bootstrap (UFBoot) replicates (Minh et al. All sequences were aligned with the Geneious Prime version 2020.0.4. All the data were downloaded from NCBI GenBank. pseudotenellum, a maximum-likelihood (ML) phylogenetic analysis was performed based on 72 protein-coding genes from 20 species in Dendrobium, with 4 species in Pleione D. pseudotenellum were consistent with those of other species in Dendrobium (Huang et al. The gene order and organization of the D. In addition, the overall GC content of the whole plastome was 37.4%, whereas the corresponding values of the LSC, SSC, and IR regions were 34.9%, 30.2%, and 43.3%, respectively. pseudotenellum encoded 125 genes, including 80 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Besides, the complete chloroplast genome of D. pseudotenellum was 149,114 bp in length, which presented a typical quadripartite structure, containing a large single-copy region (LSC 84,262 bp), a small single-copy region (SSC 12,786 bp), and two inverted repeat regions (IRA and IRB, 26,033 bp). Finally, we submitted the sequence data to GenBank with an officially accession number MN 915016. officinale Kimura et Migo (GenBank Accession No. Genome sequences were screened out and assembled with Geneious Prime version 2020.0.4 (Kearse et al. The cp genomic DNA was extracted from the fresh leaves using a modified CTAB method (Doyle and Doyle 1987), and sequenced by Illumina Hiseq 2500 platform.
#Geneious prime software code
The voucher specimen was deposited in the Herbarium of Southwest Forestry University (HSFU, specimen code of Lilu20180003). pseudotenellum were collected from Fumin County, Yunnan Province, China (25☂0′19ʺN, 102☂7′26ʺE). pseudotenellum in order to add molecular data on the phylogeny and conservation of Dendrobium. pseudotenellum was listed as an endangered species in the China Species Red List (Wang and Xie 2004 Wang et al. Owing to its narrow distribution and highly medicinal value, D. It was characterized by subterete leaves with small and white flowers, which is placed in the Sect. Whats New in Geneious R10 New features include improved cloning and plasmid viewing, alignment masking, chimera filtering, and better structural variant mapping and long read assembly.ĭiscover all of the brand new features, improvements and enhancements in Geneious R10.Dendrobium pseudotenellum Guillaum is a perennial epiphytic orchid in mountain forests and distributed in China (S. Searching, Sharing and Automation Batch BLAST against NCBI and directly search GenBank.Ĭentralize and collaborate on data with seamlessly integrated shared repositories. View and edit alignments with real-time translation and highlighting.īuild phylogenetic trees using peer-reviewed algorithms including RAxML and PAUP and adjust display settings for publication-ready graphics. Genotype microsatellite traces with automated ladder fitting and peak calling and generate tables of alleles.Īlignment and Tree Building Perform pairwise and multiple alignments of DNA or protein using trusted algorithms including MAFFT and ClustalW. Sequence and Chromatogram Analysis Trim, assemble and view Sanger sequencing trace files, correct base calls and create consensus sequences.Īutomatic annotation for gene prediction, motifs, translation and variant calling. Geneious is used by all of the top 20 universities globally (Times Higher Education, 2016) and by sixteen of the 20 largest pharmaceutical companies.Ĭomprehensive analysis of data including genome browser, contig visualization, SNP calling and RNA-Seq expression analysis. Geneious Prime Software Platform Usedįirst released in 2005, Geneious is the worlds leading bioinformatics software platform used by over 3,000 universities, institutes and companies in more than 100 countries. Discover all of the brand new features, improvements and enhancements.
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