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Large phylogenetic trees
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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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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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We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees.
15p
viwyoming2711
16-12-2020
11
1
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The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic content of mixtures of cells. Recently developed single cell sequencing technology can identify variation within a single cell.
13p
vikentucky2711
26-11-2020
11
1
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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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Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex.
10p
vikentucky2711
26-11-2020
8
1
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The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals.
4p
vikentucky2711
24-11-2020
9
1
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It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length.
14p
vioklahoma2711
19-11-2020
9
1
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During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves.
14p
vioklahoma2711
19-11-2020
13
1
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Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify “sufficiently large”.
10p
vioklahoma2711
19-11-2020
9
1
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Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a directed acyclic graph known as a phylogenetic network.
12p
vioklahoma2711
19-11-2020
7
0
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Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree.
7p
vioklahoma2711
19-11-2020
9
1
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Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes.
8p
viflorida2711
30-10-2020
13
2
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In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction.
13p
viconnecticut2711
28-10-2020
16
0
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Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but the result of uncoordinated and convenience sampling. Consequently, they can suffer from redundancy and sampling biases.
8p
viconnecticut2711
28-10-2020
13
1
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Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing “nearby” species in a reference data set, or for constructing phylogenetic trees.
17p
vicolorado2711
23-10-2020
41
1
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Leptospirosis, a zoonosis caused by Leptospira, is recognized as an emergent infectious disease. In currently, the lack of adequate diagnostic tools, vaccines are an attractive intervention strategy. In this experiment, a 550 bp fragment of large ribosomal RNA gene (16S rRNA) was sequenced and constructed phylogenetic tree from a panel of six Vietnamese pathogenic strains of Leptospira spirochetes (e.g., Pomona, Canicola, Mitis, Ictero haemohagiae, Bataviae, and Grippotyphosa).
12p
nguyenxuankha_bevandan
14-08-2020
11
1
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An attempt has been made to determine the phylogenetic relationship to trace out the evolutionary pattern of the test sequence of Xiphinema pachydermum partial 28S rRNA gene and to find out relationship of the same with other selected sequences of NCBI by constructing phylogenetic trees. Nucleotide sequence of 28S ribosomal RNA gene of Xiphinema pachydermum from Solan, Himachal Pradesh (AM779749.1) showed maximum homology of 93% with Xiphinema inaequale isolate HP 28S large subunit ribosomal RNA gene, partial sequence (HM163210.1) from Baijnath, Himachal Pradesh.
9p
trinhthamhodang3
22-02-2020
25
0
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ProDom(Corpet et al., 2000) is one of the earliest clustered protein family databases and continually updates its methods and services. Currently, it coordinates some of its larger entries with Pfam-A and uses PSI-BLAST to cluster the remaining sequences in SWISS-PROT and TrEMBL. While only large entries have been scrutinized manually, the consistency of all families is assessed by computing a series of numerical measurements. The resulting families are represented as consensus sequences and gapped multiple alignments.
10p
yasuyidol
02-04-2013
55
4
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Five healthy adult female first-generation hybrid tree frogs were produced by interspecific breeding of closely related tree frogsLitoria splendidaand L. caeruleain a cage containing large numbers of males and females of both species. Phylogenetic analysis of mitochondrial DNA sequences estab-lished the female parent to be L. splendida.
9p
inspiron33
25-03-2013
31
2
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