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Phylogenetics software

Piotr Cieślik, Józef P Knap, Lidia Piechowicz, Agata Bielawska-Drózd
Molecular epidemiology is one of the most rapidly developing research area. In the light of past and modern technologies it has gained number of typing methods based on molecular biology techniques. In this report, the subspecies differentiation of Francisella tularensis and genotyping of strains isolated in Poland and other geographic locations were investigated using real-time PCR and multispacer typing (MST) methods, respectively. In total, 49 strains of Francisella tularensis included 15 strains from Poland, for subspecies differentiation the real-time PCR method was applied...
August 14, 2018: Letters in Applied Microbiology
Daniel L Rabosky
The software program BAMM has been widely used to study rates of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common macroevolutionary rate dynamics and to estimate parameters. A recent simulation study by Meyer and Wiens (M&W) argued that (i) a simple inference framework ("MS") performs much better than BAMM, and (ii) evolutionary rates inferred with BAMM are poorly correlated with true rates...
August 12, 2018: Evolution; International Journal of Organic Evolution
Justin B Miller, Brandon D Pickett, Perry G Ridge
Motivation: Orthologous gene identification is fundamental to all aspects of biology. For example, ortholog identification between species can provide functional insights for genes of unknown function and is a necessary step in phylogenetic inference. Currently, most ortholog identification algorithms require all-versus-all BLAST comparisons, which are time consuming and memory intensive. Results: JustOrthologs is a novel approach to identifying orthologs that exploits the conservation of gene structure by using the lengths of coding sequence (CDS) regions as well as dinucleotide percentages to identify orthologs...
August 1, 2018: Bioinformatics
Yilin Zhao, Haihao Zhang, Hongbo Liu, Jie Zhang, Licun He, Hao Sun, Xiaoqin Huang, Zhaoqing Yang, Shaohui Ma
Hand, foot, and mouth disease (HFMD) is a common infectious disease caused by multiple enteroviruses (EVs) in China. To better define the etiologic agents and clinical characteristics of HFMD, we conducted this study in Yunnan, China.In this study, 1280 stool specimens were collected from pediatric patients hospitalized for treatment of HFMD in 2010. EV was detected with nested reverse transcription polymerase chain reaction and directly genotyped by gene sequencing of the viral protein 1 (VP1) region. Phylogenetic analysis was performed based on the VP1 partial gene and the clinical characteristics were analyzed using SPSS Software...
August 2018: Medicine (Baltimore)
Xuhua Xia
Missing data are frequently encountered in molecular phylogenetics, but there has been no accurate distance imputation method available for distance-based phylogenetic reconstruction. The general framework for distance imputation is to explore tree space and distance values to find an optimal combination of output tree and imputed distances. Here I develop a least-square method coupled with multivariate optimization to impute multiple missing distance in a distance matrix or from a set of aligned sequences with missing genes so that some sequences share no homologous sites (whose distances therefore need to be imputed)...
2018: PeerJ
Márton Szűcs, Ferenc Szabó, Beáta Bán, Csilla Józsa, László Rózsa, Attila Zsolnai, István Anton
Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin & Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers...
July 26, 2018: Asian-Australasian Journal of Animal Sciences
Md Atique Ahmed, Yee Ling Lau, Fu-Shi Quan
BACKGROUND: Plasmodium knowlesi a parasite of the macaques is currently the most common cause of human malaria in Malaysia. The thrombospondin-related adhesive protein (TRAP) gene is pre-erythrocytic stage antigen. It is a well-characterized vaccine candidate in Plasmodium vivax and Plasmodium falciparum, however, no study has been done in the orthologous gene of P. knowlesi. This study investigates nucleotide diversity, haplotypes, natural selection and population differentiation of full-length pktrap genes in clinical samples from Malaysia...
July 27, 2018: Malaria Journal
Thomas Flouri, Xiyun Jiao, Bruce Rannala, Ziheng Yang
The multispecies coalescent (MSC) provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program bpp includes a full-likelihood implementation of the MSC, using trans-model Markov chain Monte Carlo (MCMC) to calculate the posterior probabilities of different species trees. Bpp is suitable for analyzing multi-locus sequence datasets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus...
July 23, 2018: Molecular Biology and Evolution
S S Zhang, Y Q Tang, M X Zhang, H M Gao, C Wang, Y S Wang, S Y Han
OBJECTIVES: To analyse the genetic polymorphisms of 19 autosomal STR loci in Han population of east, middle-northwest and southwest-south Shandong and to explore its genetic relationships among the population of these three regions. METHODS: STR loci of 1 044 unrelated Han individuals in three Shandong regions were typed with a Golden e ye® DNA ID System 20A kit. The allele frequency and population genetics parameters of 19 autosomal STR loci were statistically analysed by Modified-Powerstates software...
June 2018: Fa Yi Xue za Zhi
Jun Tang, Qingquan Liu, Haiyan Yuan, Yongxia Zhang, Weilin Wang, Suzhen Huang
Iris lactea var. chinensis is a perennial herbaceous halophyte with high salt tolerance and ornamental value. Previous RNA sequencing analysis revealed a transcription factor gene IlWRKY2 expression was upregulated by salt stress. To obtain the full-length sequence, the basic characteristics of IlWRKY2 and its expression pattern under salt stress. Full-length cDNA of IlWRKY2 was cloned by 3'/5' RACE based on the intermediate sequence obtained by RNA sequencing analysis. Structure analysis of IlWRKY2 were performed by Compute pI/MW tool, PSIPRED and SWISS-MODEL analysis...
August 2018: Genes & Genomics
Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond
BACKGROUND: While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application. RESULTS: phylotree...
July 25, 2018: BMC Bioinformatics
Mariela Beatriz Reyes-Sosa, Javier Eduardo Apodaca-Hernández, María Leticia Arena-Ortiz
Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples...
November 15, 2018: Science of the Total Environment
Ling Mo, Jiandong Shi, Xiaofang Guo, Zhaoping Zeng, Ningzhu Hu, Jing Sun, Meini Wu, Hongning Zhou, Yunzhang Hu
BACKGROUND: Dengue virus (DENV) infection caused by international visitors has become a public health concern in China. Although sporadic imported cases of DENV have been documented in Yunnan, China since 2000, a complete genome sequence of dengue virus serotype 3 (DENV-3) imported from Laos is still not available. Here, we report the first complete genome sequence and genomic characterization of a DENV-3 strain (YNPE3) isolated from a patient returned from Laos. METHODS: Viral isolation from the patient's serum was performed using mosquitoes C6/36 cells...
July 24, 2018: Virology Journal
Haiming Tang, Robert D Finn, Paul D Thomas
Summary: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology terms, and PANTHER family and subfamily. The approach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. TreeGrafter takes each input query protein sequence, finds the best matching homologous family in a library of pre-calculated, pre-annotated gene trees, and then grafts it to the best location in the tree...
July 19, 2018: Bioinformatics
Emmanuel Paradis, Klaus Schliep
Summary: After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use, and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity...
July 17, 2018: Bioinformatics
Wei Fan, Changying Liu, Boning Cao, Meiling Qin, Dingpei Long, Zhonghuai Xiang, Aichun Zhao
The zinc-regulated transporters, iron-regulated transporter-like proteins (ZIPs), the natural resistance and macrophage proteins (NRAMP), the heavy metal ATPases (HMAs) and the metal tolerance or transporter proteins (MTPs) families are involved in cadmium (Cd) uptake, translocation and sequestration in plants. Mulberry ( Morus L.), one of the most ecologically and economically important (as a food plant for silkworm production) genera of perennial trees, exhibits excellent potential for remediating Cd-contaminated soils...
2018: Frontiers in Plant Science
Meenakshi Pradhan, Aruna Pal, A K Samanta, Samiddha Banerjee, R Samanta
Cytochrome B is an important polypeptide of the mitochondria helpful in energy metabolism through oxidative phosphorylation. Cytochrome B plays an immense role in the reproduction of animals and due to its mutation prone nature, it can affect the basic physiology of animals. Cytochrome B affects reproductive system in males and equally plays an important role in transferring and providing energy in the development of the embryo, zygote, and oocytes precisely in females. The present study was conducted on Ghungroo pig to study their molecular and reproductive traits and the effect of the cytochrome B gene in the female reproduction of the Ghungroo pig...
June 23, 2018: Theriogenology
Lena M Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G Lausted, Gustavo Glusman
BACKGROUND: Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these strand asymmetries arise as a result of mutational biases and selective constraints, particularly for energy efficiency. Analysis of compositional skews in a diverse set of bacteria provides a comparative context in which mutational and selective environmental constraints can be studied...
July 11, 2018: BMC Genomics
Y Sun, K Lei, Z L Xu, Y Geng
Objective: To study clinical and genetic characteristics of a Leber hereditary optic neuropathy (LHON) family with the heteroplasmic m.14484T>C mutation. Methods: A cross-sectional study. The objects of the study included a 31-year-old male LHON patient with the heteroplasmic m.14484T>C mutation (the proband) who visited Department of Ophthalmology in the Affiliated Central Hospital of Qingdao University in March 2015 and other 36 matrilineal relatives in a four-generation family (12 males and 24 females aged 2-81 years, median 27 years)...
July 11, 2018: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
Emanuelle Gabriela Gualberto de Argôlo, Thais Reis, Diego Ari Teixeira Fontes, Evonnildo Costa Gonçalves, Elane Guerreiro Giese, Francisco Tiago de Vasconcelos Melo, Jeannie Nascimento Dos Santos, Adriano Penha Furtado
Dirofilaria immitis and Acanthocheilonema reconditum are common parasites in dogs but have also been reported parasitizing humans. The differential diagnosis and epidemiological evaluation of these zoonoses are important to the development of efficient public health policies and control strategies. The purpose of this study was to carry out an epidemiological survey by using molecular methods for the specific identification of filarid parasites of domestic dogs in the Marajó mesoregion, State of Pará (PA), Brazil...
2018: PloS One
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