Mark Howison

Measurement error and variant-calling in deep Illumina sequencing of HIV

The paper develops a variant-calling pipeline for HIV sequencing, showing it reduces erroneous calls and improves accuracy compared to existing methods.

Revising transcriptome assemblies with phylogenetic information in Agalma1.0

The paper introduces treeinform, a module in Agalma1.0 that improves transcriptome assemblies by using phylogenetic analysis to correct gene misassignment errors.

Phylogenomic analyses support traditional relationships within Cnidaria

The paper uses transcriptome and genome data to analyze phylogenetic relationships within Cnidaria, supporting traditional groupings and resolving deep evolutionary relationships.

Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

The paper re-evaluates gastropod phylogenetic relationships using transcriptome and genome data, rejecting the Orthogastropoda hypothesis and proposing three alternative rooting hypotheses.