Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 9 of 9 for “"Phylogeny reconstruction"”.
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Genome-wide microbial phylogeny reconstruction with polytomy identification
… to infer large scale multi-furcating microbial phylogeny without relying on MSA (multiple sequence alignment) is greatly needed. In this dissertation work, we present two applications, ComPhy (composite distance phylogeny) and PolyPhy (phylogeny reconstruction with polytomy identification), …
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Phylogeny reconstruction of the Schoeneae (Cyperaceae) with a focus on southern African genera
… Verboom (2006). Parsimony method was used for phylogeny reconstruction. Morphological characters were then optimised on the parsimony tree using both maximum likelihood and parsimony reconstruction. The Schoeneae is not monophyletic. Scleria may be included in the Schoeneae. Schoenus is …
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Algorithms in comparative genomics
… problems: obtaining better alignments for phylogeny reconstruction, identifying related RNA sequences in genomes, and ranking Single Nucleotide Polymorphisms (SNPs) in genome-wide association studies (GWAS). Sequence alignment is a basic and widely used task in bioinformatics. Its …
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Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform
… comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We …
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A phylogenetic framework for large-scale analysis of microbial communities
… visualization of large phylogenies to the reconstruction of phylogenetic trees at unprecedented scale and resolution. Large-scale and accurate phylogeny reconstruction is crucial in tracking species at strain-level resolution across samples and phylogenetically characterizing unknown …
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Graph Based Optimization For Scientific Computing
… an efficient algorithm for unequal genome phylogeny reconstruction. Currently few methods can solve the median problem for unequal genomes which is essential in evolution tree and ancestral genome reconstruction. We present a new distance measurement model for unequal genomes and develop a …
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Phylogenetic utility of mitochondrial and nuclear genes: a case study in the diptera (true flies)
… of dipteran species. For phylogenetic tree reconstruction, mitochondrial genes performed generally inferior to nuclear genes. However, the mitochondrial genes resolved branches for which nuclear genes failed. Moreover, the combined use of mitochondrial and nuclear sequences produced superior …
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Molecular phylogenetics of the North American snake tribe Thamnophiini
… of the nine genera by performing multi-locus phylogeny and species tree estimations, and we performed constraint-based tests of monophyly of classic taxonomic designations on a gene-by-gene basis. Estimates of species trees demonstrate that both genera are paraphyletic, and this inference is …
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Phenotypic and genetic variation in an Apios americana breeding collection; and characterization of the HD-Zip gene family, involved in abiotic stress responses in Glycine max
… Hidden Markov Model guided sequence alignments. Phylogeny reconstruction enabled placement of HD-Zip sequences into four previously described subfamilies. Syntenic paralog pairs were retained following polyploidy in Glycine ~13 Mya. RNA-Seq analysis identified 20 differentially expressed HD-Zip …