DNA barcoding is a simple method for the identification of any species using a short genetic sequence from a standard genome section. The present study aimed at examining the nuclear and chloroplast diversity as well as the phylogenetic relationships of eight species of saffron including four spring-flowering and five autumn-flowering species from different parts of Iran, using the nuclear barc...

Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorit...

Blastocystis is one of the most common emerging zoonotic parasites in humans and animals. This study aimed to determine molecular prevalence subtype cattle (Bos taurus). A total 150 fresh fecal samples were collected from slaughtered various slaughterhouses Kayseri Province, Central Anatolia. Genomic DNA was extracted all used PCR analyses small subunit ribosomal RNA (SSU rRNA) gene Blastocysti...

This study represents phylogenetic analyses of two woody polygonaceous genera Calligonum and Pteropyrum using both chloroplast fragment (trnL-F) and the nuclear ribosomal internal transcribed spacer (nrDNA ITS) sequence data. All inferred phylogenies using parsimony and Bayesian methods showed that Calligonum and Pteropyrum are both monophyletic and closely related taxa. They have no affinity w...

the family magnaporthaceae considered as a single-family placed in the order magnaporthales. currently, three distinct clades are phylogenetically distinguished in this order that one is referred as the pyriculariaceae. the pyriculariaceae is characterized as a novel family having new genera, new species, new combinations and neotypification (basionym). to taxonomically evaluate this family, an...

Male Y-chromosome is currently used to estimate the paternal ancestry and migratory patterns of humans. Y-chromosomal Short Tandem Repeat(STR) segments provide important data for reconstructing phylogenetic trees. However, STR data is not widely used for phylogeny because there is not enough appropriate methodology. We propose a three-step method for analyzing large numbers of STR data and cons...

The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of oth...

We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all f...