Insertions and deletions as phylogenetic signal in an alignment-free context.

Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference.

The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.

We study the number Nk of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences-i.e.

'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.

Word-based or 'alignment-free' methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate 'pairwise' distances between nucleic-acid or protein sequences; these distance values can then be used as input for tree-reconstruction programs such as neighbor-joining.

Benchmarking of alignment-free sequence comparison methods.

Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.

Results: Here, we present a community resource (http://afproject.

Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.

Motivation: Most methods for pairwise and multiple genome alignment use fast local homology search tools to identify anchor points, i.e. high-scoring local alignments of the input sequences.