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66 results for “COI DNA barcode”
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
Fig. 3 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 3. Phylogenetic position of Macrobiotus sp., Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Fig. 1 in Application Of Dna Barcoding In Taxonomy And Phylogeny: An Individual Case Of Coi Partial Gene Sequencing From Seven Animal Species
Fig. 1. Phylogenetic position of D. lindholmi and L. a. exigua, Bayesian inference phylogenetic tree. Sequences obtained by us are written in bold.
Supplemental files to "A COI DNA Barcode Library for Anastrepha Schiner (Diptera: Tephritidae)"
<p>The attached files are the supplemental material from Moore et al., "A COI DNA Barcode Library for <em>Anastrepha </em>Schiner (Diptera: Tephritidae)". They contain various DNA sequence alignments, calculation tables, tree files, taxonomic information on <em>Anastrepha</em>, and a R script.</p>
Fig. 5 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification
Fig. 5 Percentage of template sequences coverage of the primer subsets analyzed on the second evaluation round. The red dashed line represents the complete coverage of the analyzed template sequences
Fig. 4 Primers binding position distributed along the 1,500 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification
Fig. 4 Primers binding position distributed along the 1,500 bp of the avian COI gene. A Binding position of forward primers. B Binding position of reverse primers
Fig. 3 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification
Fig. 3 Effect of the number of allowed primer-template mismatches on primer binding. Y-axis = number of primers with at least one binding event on every scenario of allowed mismatches (X-axis)
Fig. 1 Retrieved data distribution. A in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification
Fig. 1 Retrieved data distribution. A Distribution of published primers for the barcode region of the avian COI gene throughout the years. B Number of complete COI sequences available for each bird order
Fig. 2 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification
Fig. 2 Variation on the number of primers bound to the template sequences of each bird order. The dots represent data outliers
Multiple full-length variants of the Mitochondrial COI DNA Barcode Region are prevalent in North European Sawflies
Open the record for dataset details and reuse information.
Supplementary material 2 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S2 – Python script for custom grid search of hyperparameters for optimization of the neural network
Supplementary material 3 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S3 – The parameters utilized in the grid search for each of the five machine learning algorithms tested in the design of the Alfie package
Supplementary material 4 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S4 – Jupyter notebook with tutorial demonstrating how to apply the Alfie classifier in the Python programming language, and how to train custom alignment-free classifiers using the Alfie training module
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
<p>The genetic variation of the COI gene has a great effect on the final results of the species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for comprehensively appraising the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis based on different thresholds were compared among 4,288 genera (35,068 species). Besides, we also compared the match ratios obtained from two species delimitation methods: the clustering analysis (distance-based method) and the bPTP analysis (tree-based method). Furthermore, the effectiveness of two different results of the bPTP analysis: bPTP_h and bPTP_ml was also tested. Approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (> 3%), and a conservative estimate of this value is 12.05-22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of species diversity. In metabarcoding studies, a threshold of 3% can only be used to estimate the insect diversity roughly. As for the clustering analysis, the "threshOpt" or "localMinima" algorithms can provide a priori value for the researcher. Nevertheless, if the minimum interspecific genetic distance of congeneric species was greater than or equal to 2%, it is possible to avoid overestimating the species diversity based on the empirical thresholds. Besides, the match ratios of the bPTP_ml results were higher than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml results were recommended. If a proper threshold was selected, the clustering analysis may outperform the bPTP analysis.</p>
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta? attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae)
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for Drepanosticta attala and D. barbatula adults and larva plus related platystictid taxa with Sinosticta hainanense as outgroup. All voucher specimens except that of D. barbatula have a six digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p in Description of the final stadium larvae of Onychargia atrocyana Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Zygoptera: Platycnemididae), with an overview of larval characters in the Platycnemididae
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p-distance for Onychargia atrocyana using Paracnemis alluaudi and Podolestes harrissoni as outgroups. All voucher specimens have a six-digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
Figure 1. Neighbour joining COI gene tree using uncorrected p in Description of larvae of two species of Coeliccia Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Platycnemididae)
Figure 1. Neighbour joining COI gene tree using uncorrected p-distance for species of the Coeliccia borneensis-group, including both adults and larvae of C. campioni and C.flavostriata, and their sampling sites (except for Lestes dissimulans all from Sarawak, East Malaysia). Coeliccia didyma and Lestes dissimulans are used as outgroups.
FIGURE 16. Neighborjoiningtreesbasedonthe COI-5P in Morphological description and DNA barcoding of Thalassomya paraskevae sp. nov. (Diptera: Chironomidae: Telmatogetoninae) from coast of the Black Sea
FIGURE 16. Neighborjoiningtreesbasedonthe COI-5P (A) and COI-3P (B) nucleotidesequencedataof thegenus Thalassomya Schiner with Telmatogeton Schiner as an outgroup. Bootstrap support values (higher than 70%) are given above tree nodes. The sequences obtained in this study are in bold.
FIGURE 11 in DNA barcodes: Evaluating the potential of COI to diffentiate closely related species of Elachista (Lepidoptera: Gelechioidea: Elachistidae) from Australia
FIGURE 11. Pupal exuviae of the taxa of the Elachista zigzagger complex, in ventral view. A: A1; B: A2; C: A3; D: A4; E: A5; F: A6; G: B1; H: B2; I: B3.
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