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seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments
TLDR
A web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. Expand
Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga
TLDR
The genome of a bdelloid rotifer, Adineta vaga, is reported and it is shown that its structure is incompatible with conventional meiosis, and abundant evidence of gene conversion is found, which may limit the accumulation of deleterious mutations in the absence of meiosis. Expand
Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology.
TLDR
Six variable sequence markers are developed and analyzed to find out species boundaries in Hawaiian corals of the genus Pocillopora to identify five distinct mitochondrial lineages and these lineages are compatible with morphology. Expand
champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths
champuru is an interactive, user-friendly web software that facilitates the deconvolution of mixed chromatograms obtained when sequencing directly mixtures of two DNA templates of unequal lengths.Expand
Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton
TLDR
This work proposes to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring in heterozygous individuals) to visualize and delineate single-locus FFRs (sl-FFRs), and introduces a method to quantify the reliability of putative species boundaries according to the number of independent markers that support them. Expand
Guidelines for DNA taxonomy, with a focus on the meiofauna
TLDR
The recent advances in the acquisition of DNA sequence data and the analytical tools for DNA-based species delimitation are reviewed, with a focus on applications to the meiofauna. Expand
Mitochondrial sequences of Seriatopora corals show little agreement with morphology and reveal the duplication of a tRNA gene near the control region
The taxonomy of corals of the genus Seriatopora has not previously been studied using molecular sequence markers. As a first step toward a re-evaluation of species boundaries in this genus,Expand
Phase determination from direct sequencing of length‐variable DNA regions
TLDR
It is found that phase could be reconstructed from direct sequencing of mixed PCR products by combining for each individual the complementary information contained in its forward and reverse chromatograms, provided these products had different lengths. Expand
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
TLDR
Using controlled mixes of bacterial and yeast species, meta3C is developed, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Expand
The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function.
TLDR
For the first time in a cnidarian, a putative second origin of replication is described based on its secondary structure similar to the stem-loop structure of O(L), the origin of L-strand replication in vertebrates. Expand
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