Phylogenies are important for addressing various biological questions such as relationships
among species or genes, the origin and spread of viral infection and the demographic …

Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Microbial taxonomy is increasingly influenced by genome-based computational methods.
Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS …

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced
minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves …

Gene families are growing rapidly, but standard methods for inferring phylogenies do not
scale to alignments with over 10,000 sequences. We present FastTree, a method for …

The idea that all life on earth traces back to a common origin dates back at least to Charles
Darwin's Origin of Species. Ever since, biologists have tried to piece together parts of this …

Transcription factors (TFs) form the major class of regulatory genes and play key roles in
multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families …

Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …

We describe a new program for the alignment of multiple biological sequences that is both
statistically motivated and fast enough for problem sizes that arise in practice. Our F ast S …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …