Sequence alignment is just as much a part of phylogenetics as is tree building, although it is
often viewed solely as a necessary tool to construct trees. However, alignment for the …

We describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that
jointly estimates phylogeny, alignment and other parameters from unaligned sequence data …

Background RNA secondary structure comparison is a fundamental task for several studies,
among which are RNA structure prediction and evolution. The comparison can currently be …

Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative
sequence analyses in evolutionary biology. These alignments are often recognized as …

Evolutionary studies usually use a two-step process to investigate sequence data. Step one
estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods …

Background A standard procedure in many areas of bioinformatics is to use a single multiple
sequence alignment (MSA) as the basis for various types of analysis. However, downstream …

With the advent of next generation sequencing technologies, alignment and phylogeny
estimation of datasets with thousands of sequences is being attempted. To address these …

Current methods for comparing RNA secondary structures are based on tree
representations and exploit edit distance or alignment algorithms. Most of them can only …

Background Despite the long-anticipated possibility of putting sequence alignment on the
same footing as statistical phylogenetics, theorists have struggled to develop time …