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phylogenetic tree

Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

... for phylogenetic heuristic ...the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this ...of phylogenetic trees, in particular using rearrangement ...

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Characterization of Bacterial Strains Isolated Through Microbial Profiling of Urine Samples

Characterization of Bacterial Strains Isolated Through Microbial Profiling of Urine Samples

... Abstract: The present study was conducted to determine the microbial profile in urine samples. Differential and selective chromogenic culture media were used for the rapid detection, identification and enumeration of ...

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Measures of clade confidence do not correlate with accuracy of phylogenetic trees.

Measures of clade confidence do not correlate with accuracy of phylogenetic trees.

... of phylogenetic trees, which depict past relation- ships between groups of DNA or protein sequences, has valuable application in many fields of study, most commonly evolutionary and population ...the tree ...

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In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

... The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic ...the phylogenetic tree was able to cluster the ...

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Acácio Aparecido Navarrete (2) , Rodrigo Gouvêa Taketani (3) , Lucas William Mendes (4) , Fabiana de Souza Cannavan (2) , Fatima Maria de Souza Moreira

Acácio Aparecido Navarrete (2) , Rodrigo Gouvêa Taketani (3) , Lucas William Mendes (4) , Fabiana de Souza Cannavan (2) , Fatima Maria de Souza Moreira

... Selected DGGE bands were excised, macerated in sterile water and subjected to a further PCR amplification using primers 340F and 519R (∅vreås et al., 1997). The new PCR products were purified with GFX PCR DNA and the Gel ...

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Molecular Characterization of Soybean Mosaic Virus NIa Protein and its Processing Event in Bacterial Expression

Molecular Characterization of <i>Soybean Mosaic Virus</i> NIa Protein and its Processing Event in Bacterial Expression

... and phylogenetic tree: The plasmid containing NIa gene was prepared from the transformed bacterial cells using QIA Plasmid Prep Kit (QIAGEN, Germany) and used for sequencing ...Canada). Phylogenetic ...

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Evolução das quasiespécies da proteína NS5A do vírus da hepatite C genótipo 3a

Evolução das quasiespécies da proteína NS5A do vírus da hepatite C genótipo 3a

... A phylogenetic tree was constructed with the sequences from this study together with before treatment sequences from the previous study [20] (Accession numbers: EU826174 to EU826233 and from EU826249 to ...

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Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants.

Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants.

... The phylogenetic tree comparing these eight sequences to previously recorded HBV sequences in non-human primates confirms that variants recovered from chimpanzees and gorillas in Africa are distinct from ...

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Genetic characterization of Portuguese Fasciola hepatica isolates

Genetic characterization of Portuguese Fasciola hepatica isolates

... The phylogenetic tree of nad1 gene (Fig. III.22) presented a topology very similar to that of cox1 gene, with several branches and medium bootstrap values. Portuguese F. hepatica isolates are dispersed in ...

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Phenotypic and Genetic Diversity of Aeromonas Species Isolated from Fresh Water Lakes in Malaysia.

Phenotypic and Genetic Diversity of Aeromonas Species Isolated from Fresh Water Lakes in Malaysia.

... A phylogenetic tree was constructed using the rpoD gene sequence and all 102 isolates were identified as: ...the phylogenetic diversity of the ...

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Entomopathogenic fungi on Hemiberlesia pitysophila.

Entomopathogenic fungi on Hemiberlesia pitysophila.

... Five days after cultured on PDM, DNA of all fungal strains was isolated as previously reported [16] and used as template to amplify internal transcribed spacer (ITS) of rDNA as reported previously [17] using primers ITS4 ...

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Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE in China.

Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE in China.

... A phylogenetic tree was reconstructed using NJ method with 418 gag sequences, consisting of 408 China sequences and 10 CRF01_AE reference sequences isolated in Thailand, Vietnam, Cyprus, Japan and Hong ...

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Isolation and sequencing of doublesexmale abnormal 3 (DM) related transcription factor ( Dmrt ) genes from the Asian toad Bufo gargarizans

Isolation and sequencing of doublesexmale abnormal 3 (DM) related transcription factor ( Dmrt ) genes from the Asian toad Bufo gargarizans

... We obtained three female and two male B. gargarizans from Wuhu city (Anhui province, China) and humanly sacrificed them. Total genomic DNA was isolated from muscle tissues by routine protocols (Sambrook et al., 1989). To ...

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Lifang Hu 1,2, , Yingui Yang 2,

Lifang Hu 1,2, , Yingui Yang 2,

... unrooted phylogenetic tree using bootstrap analysis (1,000 repli- cates) was built from alignments of the complete protein se- quences of four cucumber CsCATs, three rice OsCATs, three Arabidopsis AtCATs, ...

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Exploring fungal diversity: Passalora, Pseudocercospora, Sirosporium and Zasmidium on Brazilian plants

Exploring fungal diversity: Passalora, Pseudocercospora, Sirosporium and Zasmidium on Brazilian plants

... 49 alignment, MrModeltest v. 2.2 (Nylander 2004) was used to select the optimal model of nucleotide substitution prior to the Bayesian Inference (BI) analysis using MrBayes v. 3.2.1 (Ronquist & Huelsenbeck 2003). The ...

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Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

... the tree species that disappear first from fragmented landscapes share similar life-history traits ...If tree life-history traits have evolved within particular lineages (trait conservatism sensu ...

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First isolation of West Nile virus in Brazil

First isolation of West Nile virus in Brazil

... midpoint phylogenetic tree of nucleotide sequences using only polyprotein coding region of 1582 West Nile virus (WNV) strains represent- ing different viral ...Different phylogenetic groups are ...

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Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution.

Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution.

... investigate phylogenetic composition of lineages and estimate divergence times ...size tree and normal distribution ...The phylogenetic tree was constructed using TreeAnnotator with a 20% ...

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Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae.

Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae.

... We also checked for the possibility of duplication events in NBS- LRRs in apple and other members of Rosaceae family (Prunus persica and Fragaria vesca). In Arabidopsis, it has been reported that NBS-LRR family follows ...

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Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

... independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja ...

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