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SVAMP: sequence variation analysis, maps and phylogeny

Raeece Naeem, Lailatul Hidayah, Mark D. Preston, Taane G. Clark, Arnab Pain
2014 Computer applications in the biosciences : CABIOS  
Allele frequency map, geographical map of isolates, Tajima's D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time.  ...  Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files.  ...  Fig. 1 . 1 Screenshot from SVAMP software shows (A) variation across 63 MRSA isolates from 15 countries, (B) allele frequency map of a variation site in the genome, (C) PCoA plot, (D) phylogenetic tree  ... 
doi:10.1093/bioinformatics/btu176 pmid:24700318 pmcid:PMC4103593 fatcat:rg5k7pftxbftjm2g23vq6nlalm

Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

Víctor M González, Núria Aventín, Emilio Centeno, Pere Puigdomènech
2014 BMC Genomics  
A phylogeny analysis of the R-genes and their comparison with syntenic sequences in other cucurbits point to a pattern of local gene amplifications since the diversification of cucurbits from other families  ...  Results: A 1-Mb sequence that contains the largest NBS-LRR gene cluster found in melon was improved using a strategy that combines Illumina paired-end mapping and PCR-based gap closing.  ...  This project was funded by the Spanish Ministerio de Ciencia e Innovación (Project BIO2010-15620), by the Spanish Ministerio de Economía y Competitividad (Project AGL2013-43244-R), and by the Fundación  ... 
doi:10.1186/1471-2164-15-1131 pmid:25523007 pmcid:PMC4378003 fatcat:p4utbm2o4ndrrgwg7z6b5an5py

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

Varvara K. Kozyreva, Chau-Linda Truong, Alexander L. Greninger, John Crandall, Rituparna Mukhopadhyay, Vishnu Chaturvedi, Daniel J. Diekema
2017 Journal of Clinical Microbiology  
The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%.  ...  The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data.  ...  E.g. mobile elements can skew the hqSNP-based phylogeny and are often excluded from the analysis.  ... 
doi:10.1128/jcm.00361-17 pmid:28592550 pmcid:PMC5527429 fatcat:w7tpef3csfewhkbruspn23c67i

Mycobacterium riyadhense clinical isolates provide insights into ancestry and adaptive evolution in tuberculosis [article]

Qingtian Guan, Musa Garbati, Sara Mfarrej, Talal AlMutairi, Alicia Smyth, Albel Singh, Shamsudeen Fagbo, John Browne, Muhammad Amin urRahman, Alya Alruwaili, Anwar Hoosen, Chie Nakajima (+5 others)
2019 biorxiv/medrxiv   pre-print
M. riyadhense shares a large number of conserved orthologues with the MTBC and contains linear and circular plasmids carrying type IV and type VII secretion systems.  ...  We conclude that M. riyadhense is an emerging mycobacterial pathogen that can serve as an experimental model to study the evolution and pathogenesis of tubercle bacilli.  ...  SNPs were called for two iterations and filtered (QD<2.0, 557 FS>60.0, SOQ>4.0, ReadPosRankSum<-8.0) with Genome Analysis Toolkit (GATK)[87]. 558 An alignment file was generated by SVAMP[88], and phylogeny  ... 
doi:10.1101/728923 fatcat:yk4adxbbb5dlbmebsryjuhde2e

The systematics of carnivorous sponges

Jon Thomassen Hestetun, Jean Vacelet, Nicole Boury-Esnault, Carole Borchiellini, Michelle Kelly, Pilar Ríos, Javier Cristobo, Hans Tore Rapp
2016 Molecular Phylogenetics and Evolution  
grateful for the opportunity not just to work with a group of organisms that I consider utterly fascinating, but also having a methodically diverse project that includes morphological taxonomy, molecular phylogeny  ...  , biogeography and even some microbial ecology.  ...  We would also like to thank Paco Cárdenas for valuable input, and Louise Lindblom, Kenneth Meland and Solveig Thorkildsen for their assistance with the lab work and phylogenetic analysis, carried out at  ... 
doi:10.1016/j.ympev.2015.08.022 pmid:26416707 fatcat:jessxebdojf3zea7bfbmv3misa

Enhancement of organic acid production from aspergillus carbonarius using a metabolic engineering approach [article]

Tore Linde
2016 Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet  
Phylogeny analysis was done with the online service from MABL (http://www.phylogeny.fr/index.cgi) using MUSCLE for alignment, PhyML for phylogeny and TreeDyn for tree rendering (Dereeper et al. 2008)  ...  Phylogenetic tree analysis based on amino acid sequence alignment, p.  ...  Materials and methods Strains and growth conditions See chapter 5 Gene analysis of the putative antiporter genes anti1 and anti4 were selected for overexpression analysis.  ... 
doi:10.5278/vbn.phd.engsci.00042 fatcat:yxoj3zbsavdhzcsbwz2ircpawu

Aalborg Universitet A new highly efficient beta-glucosidase from the novel species, Aspergillus saccharolyticus Sørensen, Annette A NEW HIGHLY EFFICIENT BETA-GLUCOSIDASE FROM THE NOVEL SPECIES, ASPERGILLUS SACCHAROLYTICUS A NEW HIGHLY EFFICIENT BETA-GLUCOSIDASE FROM THE NOVEL SPECIES, ASPERGILLUS SACCHAROLYTICUS

Annette Sørensen, Annette Sørensen
2010 unpublished
Professor Henrik Christensen, University of Copenhagen is thanked for his assistance in relation to phylogeny.  ...  Financial support from Danish Council for Strategic Research and DANSCATT is acknowledged.  ...  The variation in sequence data observed between A. saccharolyticus and A. homomorphus is the same as the variation between A. homomorphus and the smaller clade(s) of A. aculeatinus, A. uvarum, A. japonicus  ... 
fatcat:2qyb6nqkhvd3tpkzldmo7daduq

The genus Cladosporium

K. Bensch, U. Braun, J.Z. Groenewald, P.W. Crous
2012 Studies in Mycology  
It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str.  ...  translation elongation factor 1-α gene sequences) diagnostic for individual species.  ...  We are very grateful to the directors and curators for loaning type material and other collections in their keeping  ... 
doi:10.3114/sim0003 pmid:22815589 pmcid:PMC3390897 fatcat:ff67euqcojhyxefij6fmbzmbje

A taxonómiában használt morfológiai bélyegek értékelése molekuláris filogenetikai eredmények segítségével a pókhálósgombák nemzetségénél

Bálint Dima, Gábor Kovács M.
2019
DNA (ITS) sequence 12 collections have been sequenced. The species shows a minor infraspecific variation of 1-2 nucleotides.  ...  DNA (ITS) sequence. Three collections have been sequenced and they were identical.  ... 
doi:10.15476/elte.2019.144 fatcat:wjghbm2hirf3zmvjgj55fzalry

vU*m77r* *tynm>*dh

> Henning, Weimarck
unpublished
The pathways of sexual and apomictic development have been worked out. and criteria for identifying each type of behaviour during different periods of embryo sac growth have been formulated.  ...  for cheeking the identification Wc wish to thank the Queens University of Belfast for the provision i»l the controlled environment equipment in «huh some of the experimental work «as carried out and Hit  ...  Mechanical analysis has been performed as combined sedimenlalionand pipette analysis according to Tamra (1934 I? ulk s p c c i f i c gråvit y, s.  ... 
fatcat:neqpeoebrvgprl4265gl4e5me4