A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
SVAMP: sequence variation analysis, maps and phylogeny
2014
Computer applications in the biosciences : CABIOS
Preserved Fulltext
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
2014
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2017
Journal of Clinical Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2019
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2016
Molecular Phylogenetics and Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2016
Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2010
unpublished
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2012
Studies in Mycology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2019
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
unpublished
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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