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Phylogenetics software

Ya-Lan Huang, Da-Na Huang, Wei-Hua Wu, Fan Yang, Xiao-Min Zhang, Miao Wang, Yi-Jun Tang, Qian Zhang, Li-Fei Peng, Ren-Li Zhang
BACKGROUND: Two health concerns primarily related to triatomine bugs are transmission of Trypanosoma cruzi through infective feces, and allergic reactions induced by triatomine bites. In the Southwestern United States, reduviid bugs bites commonly cause insect allergy. In South China, four cases of anaphylactic shock have been reported after this bite exposure. To further classify the species of these bugs and confirm the sensitization of the triatomine saliva, we caught triatomine bugs from the region where the bites occurred and performed phylogenetic and immunohistochemical (IHC) analysis...
December 11, 2018: Infectious Diseases of Poverty
Chris-Andre Leimeister, Jendrik Schellhorn, Svenja Dörrer, Michael Gerth, Christoph Bleidorn, Burkhard Morgenstern
Word-based or 'alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM...
December 7, 2018: GigaScience
Duarte Gouveia, Christine Almunia, Yannick Cogne, Olivier Pible, Davide Degli-Esposti, Arnaud Salvador, Susana Cristobal, David Sheehan, Arnaud Chaumot, Olivier Geffard, Jean Armengaud
Anthropogenic pollutants are found worldwide. Their fate and effects on human and ecosystem health must be appropriately monitored. Today, ecotoxicology is focused on the development of new methods to assess the impact of pollutant toxicity on living organisms and ecosystems. In situ biomonitoring often uses sentinel animals for which, ideally, molecular biomarkers have been defined thanks to which environmental quality can be assessed. In this context, high-throughput proteomics methods offer an attractive approach to study the early molecular responses of organisms to environmental stressors...
December 6, 2018: Journal of Proteomics
Hugo López-Fernández, Pedro Duque, Sílvia Henriques, Noé Vázquez, Florentino Fdez-Riverola, Cristina P Vieira, Miguel Reboiro-Jato, Jorge Vieira
Useful insight into the evolution of genes and gene families can be provided by the analysis of all available genome datasets rather than just a few, which are usually those of model species. Handling and transforming such datasets into the desired format for downstream analyses is, however, often a difficult and time-consuming task for researchers without a background in informatics. Therefore, we present two simple and fast protocols for data preparation, using an easy-to-install, open-source, cross-platform software application with user-friendly, rich graphical user interface (SEDA; http://www...
December 3, 2018: Interdisciplinary Sciences, Computational Life Sciences
Vincenzo Bonnici, Rosalba Giugno, Vincenzo Manca
BACKGROUND: Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. The retrieval of a complete gene distribution among a class of genomes is an NP-hard problem because computational costs increase with the number of analyzed genomes, in fact, all-against-all gene comparisons are required to completely solve the problem. In presence of phylogenetically distant genomes, due to the variability introduced in gene duplication and transmission, the task of recognizing homologous genes becomes even more difficult...
November 30, 2018: BMC Bioinformatics
Melanie J Hopkins, Katherine St John
The use of discrete character data for disparity analyses has become more popular, partially due to the recognition that character data describe variation at large taxonomic scales, as well as the increasing availability of both character matrices co-opted from phylogenetic analysis and software tools. As taxonomic scope increases, the need to describe variation leads to some characters that may describe traits not found across all the taxa. In such situations, it is common practice to treat inapplicable characters as missing data when calculating dissimilarity matrices for disparity studies...
November 28, 2018: Proceedings. Biological Sciences
Mohammad Hadi Karbalaie Niya, Hossein Ajdarkosh, Fahimeh Safarnezhad Tameshkel, Mahshid Panahi, Maryam Tabasi, Behnaz Bouzari, Mahdi Alemrajabi, Hossein Keyvani
Background: Colorectal cancer (CRC) as a worldwide human health concern is identified being a multifactorial subject that infection with specific viral particles such as oncogenic viruses is research interest. Human bocavirus (HBoV) as a recent isolated virus has been investigated in many respiratory and enteric diseases but rare studies evaluates it in tissue specimens especially in cancerous sections. The aim of this study was to detect the presence of HBoV genome and its genotyping in CRC patient’s tissue and compare the result with matched healthy control group tissue...
November 29, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
Daniel L Rabosky
A recent pair of articles published in the journal Evolution presented a test for assessing the validity of hierarchical macroevolutionary models. The premise of the test is to compare numerical point estimates of parameters from two levels of analysis; if the estimates differ, the hierarchical model is purportedly flawed. The articles in question (Meyer and Wiens 2017; Meyer et al. 2018) apply their proposed test to BAMM, a scientific software program that uses a Bayesian mixture model to estimate rates of evolution from phylogenetic trees...
November 27, 2018: Systematic Biology
Ritika Ramani, Katie Krumholz, Yi-Fei Huang, Adam Siepel
Summary: The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment...
November 27, 2018: Bioinformatics
Jun-Hui Yu, Wei-Wu Shi, Mei-Ying Zhou, Jia-Mei Liu, Qiu-Yue Han, Hui-Hui Xu
It is well recognized that the association of human papillomavirus (HPV) and cervical carcinogenesis is based on the presence of HPV DNA sequence. The E6 and E7 oncoproteins encoded by high-risk HPV types play a key role in carcinogenesis. HPV58 type accounts for a larger share of cervical disease in China, whereas data on HPV58 genetic variability in China is limited. We aimed to evaluate the diversity of HPV58 genetic variants by sequencing the entire E6 and E7 genes. Phylogenetic trees were constructed by Maximum likelihood method by MEGA 5...
November 21, 2018: Gene
Y H Wan, L Zhuang, Q N Zheng, L J Ren, L Fu, W J Jiang, G P Tang, D Z Zhang, S J Li
Objective: To understand the molecular characteristics of hemagglutinin (HA) and neuraminidase (NA) as well as the disease risk of influenza virus A H7N9 in Guizhou province. Methods: RNAs were extracted and sequenced from HA and NA genes of H7N9 virus strains obtained from 18 cases of human infection with H7N9 virus and 6 environmental swabs in Guizhou province during 2014-2017. Then the variation and the genetic evolution of the virus were analyzed by using a series of bioinformatics software package. Results: Homology analysis of HA and NA genes revealed that 2 strains detected during 2014-2015 shared 98...
November 10, 2018: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Hai Yun Li, Tuo Yao, Jian Gui Zhang, Ya Min Gao, Ya Chun Ma, Xiao Wen Lu, Hui Rong Zhang, Xiao Lei Yang
To explore the distribution of bacterial community and its relationship with soil environmental factors in degraded alpine grasslands in the eastern Qilian Mountains, we analyzed the changes of bacterial community structure and diversity across lightly, moderately and severely degraded grasslands by using high-throughput sequencing technology. Redundancy analysis (RDA) was performed to analyze the relationship between soil bacterial communities and soil environmental factors by using CANOCO 4.5 software. The results showed that there were significant differences in soil physicochemical properties among different degraded alpine grasslands...
November 2018: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
Christophe Guyeux, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot, Michel Salomon
BACKGROUND: To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More particularly, as the principal forces that have led to major structural changes are genome rearrangements (such as translocations, fusions, and so on), understanding their underlying mechanisms, among other things via the ancestral genome reconstruction, are essential...
November 20, 2018: BMC Systems Biology
Shichuang Zhang, Yuexia Tong, Yingjun Li, Zong-Ming Cheng, Yan Zhong
INTRODUCTION: The high-affinity potassium transporter (HKT) gene family is implicated in the regulation of response to salt stress in different plants. Yet, knowledge remains very limited for them in the Rosaceae species. The whole genome sequences of the five Rosaceae species, including Fragaria vesca (woodland strawberry), Malus domestica (apple), Pyrus communis (pear), Prunus mume (mei) and Prunus persica (peach), give the opportunity to uncover the evolutionary pattern of the HKT genes among Rosaceae genomes...
November 19, 2018: Genes & Genomics
Yan-Ping Xing, Si-You Chen, Liang Xu, Yong-Man Liang, Jia-Hao Wang, Bing Wang, Tao Liu, Ting-Guo Kang
Fructus Arctii is a traditional Chinese medicine. The main counterfeit species are the seeds of Arctium tomentosum, Onopordum acanthium, Silybum marianum, Saussurea costus, Amorpha fruticosa. Traditional identification methods or molecular barcoding techniques can identify Fructus Arctii and its counterfeit species. However, the identification of the mixture of it and its spurious species is rarely reported. In this paper, we sequenced the ITS2 sequences of Fructus Arctii and 5 kinds of spurious species mix powder by high-throughput sequencing to identify the mixed powder species and providing new ideas for the identification of Fructus Arctii mix powder...
October 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
(no author information available yet)
No abstract text is available yet for this article.
November 1, 2018: Genome Biology and Evolution
Dan Yao, Hainan Wu, Yuhua Chen, Wenguo Yang, Hua Gao, Chunfa Tong
Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents...
November 14, 2018: Briefings in Bioinformatics
Ravindra P Turankar, Vikram Singh, Hariom Gupta, Vinay Kumar Pathak, Madhvi Ahuja, Itu Singh, Mallika Lavania, Amit Dinda, Utpal Sengupta
Non-tuberculous mycobacteria (NTM) are environmental mycobacteria found ubiquitously in nature. The present study was conducted to find out the presence of various species of NTM in leprosy endemic region along with Mycobacterium (M) leprae. Water and wet soil samples from the periphery of ponds used by the community were collected from districts of Purulia of West Bengal and Champa of Chhattisgarh, India. Samples were processed and decontaminated followed by culturing on Lowenstein Jensen (LJ) media. Polymerase chain reaction (PCR) was performed using 16S rRNA gene target of mycobacteria and species was confirmed by sequencing method...
November 13, 2018: Infection, Genetics and Evolution
Erik M Volz, Igor Siveroni
Population genetic modeling can enhance Bayesian phylogenetic inference by providing a realistic prior on the distribution of branch lengths and times of common ancestry. The parameters of a population genetic model may also have intrinsic importance, and simultaneous estimation of a phylogeny and model parameters has enabled phylodynamic inference of population growth rates, reproduction numbers, and effective population size through time. Phylodynamic inference based on pathogen genetic sequence data has emerged as useful supplement to epidemic surveillance, however commonly-used mechanistic models that are typically fitted to non-genetic surveillance data are rarely fitted to pathogen genetic data due to a dearth of software tools, and the theory required to conduct such inference has been developed only recently...
November 2018: PLoS Computational Biology
Onur Ozturk, Sanem Arikan, Ayfer Atalay, Erol O Atalay
BACKGROUND: β-Globin gene cluster haplotypes associated with the Hb D-Los Angeles mutation have been reported in many different locations in different populations including Italy, Iran, Thailand, Belgium, Mexico, Holland, and Turkey. In this study, we have identified genetic relationships and formation periods between the haplotypes reported in the world regarding the Hb D-Los Angeles. METHODS: We comparatively analyzed the RFLP (restriction fragment length polymorphism) data in Denizli region and world populations using Arlequin 3...
November 11, 2018: Molecular Genetics & Genomic Medicine
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