SWPhylo–a novel tool for phylogenomic inferences by comparison of oligonucleotide patterns and integration of genome-based and gene-based phylogenetic trees
X Yu, ON Reva - Evolutionary Bioinformatics, 2018 - journals.sagepub.com
Modern phylogenetic studies may benefit from the analysis of complete genome sequences
of various microorganisms. Evolutionary inferences based on genome-scale analysis are …
of various microorganisms. Evolutionary inferences based on genome-scale analysis are …
Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics
A key challenge in microbial phylogenomics is that microbial gene families are often affected
by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial …
by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial …
Phylogenomics for studies of microbial evolution
SGE Andersson, HH Fuxelius - Encyclopedia of Genetics …, 2004 - Wiley Online Library
The classification of microorganisms represents a major challenge, the basis of which has
been an issue of debate for the past 100 years. Phylogenetic inference based on rRNA …
been an issue of debate for the past 100 years. Phylogenetic inference based on rRNA …
Comparative phylogenomics: a strategy for high-throughput large-scale sub-genomic sequencing projects for phylogenetic analysis
AJ Phillips - Techniques in Molecular Systematics and Evolution, 2002 - Springer
Since rapid sequencing of bacterial genomes is currently feasible, it has been suggested
that sequences for entire genomes of complex organisms will be commonplace in the future …
that sequences for entire genomes of complex organisms will be commonplace in the future …
[PDF][PDF] Construction of a phylogenetic matrix: Scripts and guidelines for phylogenomics
Phylogenomics is a new field that infers evolutionary relationships of taxa at the genome-
scale level. The increment of molecular data may raise the potential bias as the limiting …
scale level. The increment of molecular data may raise the potential bias as the limiting …
Assembling a reference phylogenomic tree of bacteria and archaea by summarizing many gene phylogenies
Phylogenomics is the inference of phylogenetic trees based on multiple marker genes
sampled in the genomes of interest. An important challenge in phylogenomics is the …
sampled in the genomes of interest. An important challenge in phylogenomics is the …
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics
Background The availability of sequences from whole genomes to reconstruct the tree of life
has the potential to enable the development of phylogenomic hypotheses in ways that have …
has the potential to enable the development of phylogenomic hypotheses in ways that have …
Telling the whole story in a 10,000-genome world
RG Beiko - Biology Direct, 2011 - Springer
Background Genome sequencing has revolutionized our view of the relationships among
genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT) …
genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT) …
A Guide to Phylogenomic Inference
JSL Patané, J Martins Jr, JC Setubal - Comparative Genomics: Methods …, 2024 - Springer
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. Phylogenomics has significant …
account whole genomes or large fractions of genomes. Phylogenomics has significant …
Genome trees and the nature of genome evolution
Genome trees are a means to capture the overwhelming amount of phylogenetic information
that is present in genomes. Different formalisms have been introduced to reconstruct …
that is present in genomes. Different formalisms have been introduced to reconstruct …