Ashley Craig

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

Analysis of multiple sequence alignments can generate vital, testable hypotheses in regards to the phylogenetic historical past and mobile perform of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, lengthy genomic DNA sequences rapidly and with good sensitivity . Alignments are computed between a contiguous reference sequence and a number of secondary sequences, …

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Read More »

The DNA transposon Minos as a tool for transgenesis and functional genomic analysis in vertebrates and invertebrates.

The DNA transposon Minos as a tool for transgenesis and functional genomic analysis in vertebrates and invertebrates.

Transposons are highly effective instruments for conducting genetic manipulation and functional research in organisms which are of scientific, financial, or medical curiosity. Minos, a member of the Tc1/mariner household of DNA transposons, displays a low insertional bias and transposes with excessive frequency in vertebrates and invertebrates. Its use as a tool for transgenesis and genome …

The DNA transposon Minos as a tool for transgenesis and functional genomic analysis in vertebrates and invertebrates. Read More »

PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences.

PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences.

BACKGROUNDPeriodic spacing of brief adenine or thymine runs phased with DNA helical interval of ~10.5 bp is related to intrinsic DNA curvature and deformability, which play essential roles in DNA-protein interactions and in the group of chromosomes in each eukaryotes and prokaryotes. Local variations in DNA sequence periodicity have been linked to variations in gene …

PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences. Read More »

A common tool for simulating trees is the birth–death

Tree simulation is an important tool for exploring the processes

TreeMan is an S4 class that encodes a phylogenetic tree utilizing a node listing. The benefit of a node listing is the sooner computational processing, and the prepared capability to trace nodes between manipulations and vectorise or parallelise large-scale tree manipulations. The treeman bundle introduces new terminology to explain totally different components of a tree …

Tree simulation is an important tool for exploring the processes Read More »

Tree simulation: generating trees using different models of evolution

Tree simulation: generating trees using different models of evolution

Tree simulation is a crucial instrument for exploring the processes that will have generated biodiversity. A typical instrument for simulating trees is the start–dying simulation or equals-rates Markov mannequin (ERMM) that randomly removes and provides tips about a tree Many publications have independently explored alterations of the ERMM, similar to modifying the charges of speciation …

Tree simulation: generating trees using different models of evolution Read More »

The TreeMan object in R is an S4 formal class

The TreeMan object in R is an S4 formal class

The TreeMan object in R is an S4 formal class whose foremost information slot is an inventory—which in R is a vector whose components might be named. All nodes in a TreeMan object are named components in this record (ndlst). Each node normally incorporates the next information slots: the node ID (id), the size of …

The TreeMan object in R is an S4 formal class Read More »

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

BACKGROUNDPhylogenetic trees are hierarchical constructions used for representing the inter-relationships between organic entities. They are the commonest device for representing evolution and are important to a variety of fields throughout the life sciences. The manipulation of phylogenetic trees-in phrases of including or eradicating tips-is usually carried out by researchers not simply for causes of administration …

treeman: an R package for efficient and intuitive manipulation of phylogenetic trees Read More »

Scroll to Top