An efficient, nonphylogenetic method for detecting genes sharing evolutionary signals in phylogenomic data sets
LT Rangel, SM Soucy, JC Setubal… - Genome Biology and …, 2021 - academic.oup.com
Assessing the compatibility between gene family phylogenies is a crucial and often
computationally demanding step in many phylogenomic analyses. Here, we describe the …
computationally demanding step in many phylogenomic analyses. Here, we describe the …
Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life
Assessing the phylogenetic compatibility between individual gene families is a crucial and
often computationally demanding step in many phylogenomics analyses. Here we describe …
often computationally demanding step in many phylogenomics analyses. Here we describe …
Testing congruence in phylogenomic analysis
Phylogenomic analyses of large sets of genes or proteins have the potential to revolutionize
our understanding of the tree of life. However, problems arise because estimated …
our understanding of the tree of life. However, problems arise because estimated …
Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time
CE Blank - Archaea, 2012 - Wiley Online Library
Phylogenomic analyses of archaeal genome sequences are providing windows into the
group's evolutionary past, even though most archaeal taxa lack a conventional fossil record …
group's evolutionary past, even though most archaeal taxa lack a conventional fossil record …
New methods to calculate concordance factors for phylogenomic datasets
We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
Dissecting incongruence between concatenation-and quartet-based approaches in phylogenomic data
Topological conflict or incongruence is widespread in phylogenomic data. Concatenation-
and coalescent-based approaches often result in incongruent topologies, but the causes of …
and coalescent-based approaches often result in incongruent topologies, but the causes of …
Conserved genes, sampling error, and phylogenomic inference
Disagreement or conflict among phylogenetic hypotheses obtained by analysis of large,
genomewide data sets has incited debate over potential benefits, pitfalls, and best practices …
genomewide data sets has incited debate over potential benefits, pitfalls, and best practices …
Statistics and truth in phylogenomics
Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
S Hartmann, TJ Vision - BMC evolutionary biology, 2008 - Springer
Background While full genome sequences are still only available for a handful of taxa, large
collections of partial gene sequences are available for many more. The alignment of partial …
collections of partial gene sequences are available for many more. The alignment of partial …
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …
relationships, but this is challenged by the discordant evolution of individual genes. Here we …