COITrees implements a data structure for very fast overlap queries of a static set of integer intervals, with genomic intervals in mind. Borrowing from cgranges, this data structure stores intervals in contiguous memory, but improves query performance by storing the nodes in in-order van Emde Boas layout.

Feb 5, 2016 · The mitochondrial cytochrome oxidase subunit 1 (COI) gene is one of the most popular markers used for molecular systematics. Fragments of this gene are often used to infer phylogenies, particularly the region near the 5'-end, which is …

coitrees implements a fast static interval tree data structure with genomic data in mind. The data structure used a fairly standard interval tree, but with nodes stored in van Emde Boas layout, which improves average cache locality, and thus query performance.

In this study, we directly compared the relative effectiveness of COI, 16S ribosomal DNA (rDNA), nuclear ribosomal internal transcribed spacer 2 (ITS2) and 12S rDNA for tick species identification. A total of 307 sequences from 84 specimens representing eight tick species were acquired by PCR.

Oct 13, 2016 · In 2003, a standardized 658 bp fragment of the mitochondrial cytochrome C oxidase subunit I gene (cox1 or COI) was proposed as a universal marker for species identification – to be used as...

COI, which stands for cytochrome c oxidase subunit I, encodes part of an enzyme that is important for cellular respiration. COI has been sequenced for many animals, and its sequences are often unique to a particular species.

Jul 25, 2017 · Here, we analyzed 95 specimens from 11 morphologically distinct species of benthic ctenophores from the Red Sea and Sulu Sea, and tested selected regions of four genetic markers (ITS1, 18S rRNA,...

... phylogenetic tree based on the mitochondrial COI gene sequences of 42 species (Figure 1) shows an arrangement of investigated species, which is in agreement with the classification system...

Phylogenetic tree (COI + 12S) for coral-associated barnacles based on maximum likelihood (ML) analysis of the two mitochondrial gene datasets. ML trees were constructed with RaxML 8.0.2 using...

The first is generated from a distance matrix using the COI mitochondrial gene; the second is generated from the 16S ribosomal subunit mitochondrial gene. Map your character state changes onto each tree and calculate the consistency index.