Transposable elements (TEs) may contribute to evolutionary innovations through the
rewiring of networks by supplying ready-to-use cis regulatory elements. Genes on the …

Multiple sequence alignment (MSA) of DNA, RNA, and protein sequences is one of the most
essential techniques in the fields of molecular biology, computational biology, and …

Motivation: We present a new feature of the MAFFT multiple alignment program for
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …

Multiple sequence alignments are fundamental to many sequence analysis methods. Most
alignments are computed using the progressive alignment heuristic. These methods are …

Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse
cellular processes. Determining the function of individual lincRNAs remains a challenge …

Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in
mammals, few have been functionally characterized, leading to debate about their biological …

Background Multiple genome alignment remains a challenging problem. Effects of
recombination including rearrangement, segmental duplication, gain, and loss can create a …

Methanogenic and methanotrophic archaea play important roles in the global flux of
methane. Culture-independent approaches are providing deeper insight into the diversity …

Background We recently described FastTree, a tool for inferring phylogenies for alignments
with up to hundreds of thousands of sequences. Here, we describe improvements to …

Methods for detecting nucleotide substitution rates that are faster or slower than expected
under neutral drift are widely used to identify candidate functional elements in genomic …