Haplotype reconstruction
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Ablepharus Lichtenstein, 1823, which includes ten species, is distributed in eastern Europe and Asia. Four species are recorded in Turkey: A. kitaibelii, A. chernovi, A. bivittatus, and A. budaki. After molecular and morphological studies in Anatolia, the phylogenetic relationship of the genus is still very complicated. Here, we investigate the taxonomic status of Ablepharus in Anatolia using morphological and molecular methods. The genetic structure of Ablepharus populations in Anatolia was analyzed using both the nuclear (CMOS) and mitochondrial (cyt b and COI) gene regions.
12p dolomite36 30-12-2021 16 1 Download
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Single individual haplotype problem refers to reconstructing haplotypes of an individual based on several input fragments sequenced from a specified chromosome.
15p vikentucky2711 24-11-2020 8 1 Download
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Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled or untagged individuals, especially when the reconstruction of full length haplotypes can be unreliable.
12p vioklahoma2711 19-11-2020 12 1 Download
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Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes.
11p viconnecticut2711 28-10-2020 9 1 Download
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Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity.
13p vicolorado2711 23-10-2020 8 1 Download
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A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype.
9p vicolorado2711 23-10-2020 10 1 Download
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Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads.
18p vicolorado2711 22-10-2020 5 0 Download
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The fragmentation of DNA in historical specimens is very common, so obtaining sequences that allow molecular identification and the study of diversity is quite challenging. In this study, we used preserved and fresh specimens of the fruit fly genus Anastrepha, a genus of economic impact of fruit crops of the Neotropic.
12p trinhthamhodang1 14-11-2019 18 0 Download