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Phylogenetic reconstruction
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Reconstructing phylogenetic trees from protein sequences normally requires empirical amino acid substitution models to calculate the likelihood of trees or genetic distances between species. The tree of life is classified into three domains of Eukaryotes, Archaea, and Bacteria. The amino acid substitution models have been intensively studied for decades, but few are related to Bacteria. Rooting bacterial trees remains a challenging problem in the phylogenetic analysis due to the long branch separating Bacteria and other domains.
14p
dianmotminh02
03-05-2024
4
2
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Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.
329p
tracanhphuonghoa1007
22-04-2024
10
2
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Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and development of new antibiotics.
19p
vibransone
28-03-2024
5
2
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Ebook "Introduction to mathematical methods in bioinformatics" looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.
305p
tachieuhoa
28-01-2024
6
2
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The phylogenetic relationship of 83 taxa of Santalaceae s.l. was reconstructed based on the molecular data sets including the nuclear ribosomal (small and large subunit rDNA) and the chloroplast rbcL, matK, and trnL-F regions. The Maximum likelihood (ML) and Bayesian inference (BI) methods were used to build the phylogenetic trees.
8p
viellenkullman
13-05-2022
6
1
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Exploring the phylogenetic relationships between taxa provides important information for science. The phylogenetic study of Macrosolen was conducted based on molecular data sets of 27 taxa with five DNA regions including chloroplast rbcL, matK, and trnL-F and nuclear ribosomal (small subunit rDNA and large subunit rDNA) regions to reconstruct the phylogenetic relationship of Macrosolen.
7p
viginnirometty
04-05-2022
17
1
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Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones.
15p
viarchimedes
26-01-2022
6
0
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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
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Understanding disjunct distribution patterns in the Balkan Peninsula and Anatolia is important in order to reconstruct robust biogeographical hypotheses. This is instrumental in understanding the recolonization patterns of Europe during the Quaternary glaciation/interglaciation periods and the potential role of Anatolia as a refugium. Unfortunately, only a few studies have been conducted to uncover such processes. Here, we used all eight species of the genus Bornmuellera (Brassicaceae) with a scattered distribution in the Balkans and Anatolia to reconstruct its biogeographic history.
11p
tudichquannguyet
29-11-2021
5
1
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Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods.
8p
vilarryellison
29-10-2021
11
0
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Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny.
18p
vibeauty
23-10-2021
5
1
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Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.
11p
vitzuyu2711
29-09-2021
8
1
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Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA.
14p
vitzuyu2711
29-09-2021
21
1
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Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved.
15p
viansan2711
30-07-2021
10
1
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Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains.
10p
vijeeni2711
30-06-2021
8
1
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Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2.
11p
vilichoo2711
25-06-2021
14
1
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Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored.
15p
vijichea2711
28-05-2021
11
1
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Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances.
9p
viwyoming2711
16-12-2020
14
1
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Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates.
16p
viwyoming2711
16-12-2020
14
0
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Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation.
31p
vikentucky2711
26-11-2020
13
1
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