In this review, we discuss the current status and future challenges for fully elucidating the
fungal tree of life. In the last 15 years, advances in genomic technologies have …

Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from
erroneous inference of homology and saturation of substitutions, are thought to negatively …

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder's
high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted …

The standard bootstrap (SBS), despite being computationally intensive, is widely used in
maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap …

Phylogenomic studies using genome-scale amounts of data have greatly improved
understanding of the tree of life. Despite the diversity, ecological significance, and …

We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as
genetically diverse as plants or animals. To understand budding yeast evolution, we …

Our understanding of phylogenetic relationships among bony fishes has been transformed
by analysis of a small number of genes, but uncertainty remains around critical nodes …

To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …