Nematode Small Subunit Phylogeny Correlates with Alignment Parameters

Nematode small subunit phylogeny correlates with alignment parameters.

The number of nuclear small subunit (SSU) ribosomal RNA (rRNA) sequences for Nematoda has increased dramatically in recent years, and although their use in constructing phylogenies has also increased, relatively little attention has been given to their alignment. Here we examined the sensitivity of the nematode SSU data set to different alignment parameters and to the removal of alignment ambig...

System analysis and nematode phylogeny.

Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences.

The Mollusca represent one of the most morphologically diverse animal phyla, prompting a variety of hypotheses on relationships between the major lineages within the phylum based upon morphological, developmental, and paleontological data. Analyses of small-ribosomal RNA (SSU rRNA) gene sequence have provided limited resolution of higher-level relationships within the Mollusca. Recent analyses ...

Joint Bayesian estimation of alignment and phylogeny.

We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are con...

Alignment Free String Distances for Phylogeny

In this paper, we compare the accuracy of four string distances to recover correct phylogenies of complete genomes . These distances are based on common words shared by raw genomic sequences and do not require preliminary processing steps such as gene identification or sequence alignment. Moreover, they are computable in linear time. The first distance is based on Maximum Significant Matches. T...