SUMMARY Phylogenetic Web Profiler (PWP) is a web-based service designed to perform phylogenetic profiling of proteins against genomes. The current version offers a selection of 63 completed genomes and available plasmids as annotated in the PEDANT genome database. Unlike currently available applications, this tool offers several choices of ortholog prediction parameters including E-value cutoff...

• Midbrain dopaminergic neuron transcription factors modulate the long-term survival and maintenance of these neurons. Understanding developmental pathways might lead to a better insight into their degeneration in Parkinson's disease. Phylogenetic profiling was used identify molecular interactions correlated with factors. Two distinct evolutionary pathways, pertaining early late novel links wer...

Retroviral recombination is an issue in studies of HIV-1 evolution within individuals who harbor a genetically diverse virus population. The nature of retroviral replication is such that recombinant HIV-1 genomes would be expected to be a complex mosaic of parental sequences. However, given the comparatively low levels of virus diversity within an individual, relatively few recombination breakp...

Micro-indels are small insertion or deletion events (indels) that occur during genome evolution. The study of micro-indels is important, both in order to better understand the underlying biological mechanisms, and also for improving the evolutionary models used in sequence alignment and phylogenetic analysis. The inference of micro-indels from multiple sequence alignments of related genomes pos...