Sequence alignments and phylogenetic analysis
DendroBlast: approximate phylogenetic trees in the absence of multiple sequence alignments
... multiple sequence alignments with addition of alignment induced ...in phylogenetic analysis for alignments to be subject to trimming before ...mis-aligned sequence and hence ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... Such alignments can be improved by increasing the sig- nal-to-noise ratio through exclusion of noisy ...improve phylogenetic analysis and car- ried out manually, are common ...large-size ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... by sequence constraints due to environmental pres- sure can produce a considerable amount of phylo- genetic noise in the data and so-called “bad” and phylogenetically misleading ...improve phylogenetic ...
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PHYLOGENETIC ANALYSIS
... protein sequence to the SWISS-PROT/TREMBL databases using BLAST2 and then allows user-defined phylogenetic analyses to be performed on selected sequences from the BLAST ...multiple sequence ...
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SeqTools: visual tools for manual analysis of sequence alignments
... reference alignments and annotation. Annotators need to be able to view sequence alignments in ...of sequence alignment: Blixem is a many-to-one browser of pairwise alignments, ...
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Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
... whole sequence segments of equal length with each other. Alignments are composed from gap-free segment pairs, so-called fragment alignments or just ...
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ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
... Horizontal dependencies are immediately visible. For example, all Ciona sequences (selected in red) have a Met in position 241 and also exclusively have a Glu residue in position 246 and a His at position 248. This ...
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Sequence and Phylogenetic Analysis of SSU rRNA Gene of Five Microsporidia
... of Phylogenetic Tree and Analysis of SSU rRNA Gene Sequences The SSU rRNA gene sequences were aligned using the ‘‘ClustalX ...program. Phylogenetic trees based on the resultant alignments ...
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IVisTMSA: INTERACTIVE VISUAL TOOLS FOR MULTIPLE SEQUENCE ALIGNMENTS
... test alignments against a single reference ...test alignments are displayed in tabular ...test alignments in form of bar, pie and line ...test alignments have conserved ...multiple ...
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Target Sequence Capture of Nuclear-Encoded Genes for Phylogenetic Analysis in Ferns
... adaptive quality trim with a target length of 10 nucleotides and strictness of 0.2, and discarded any reads trimmed to under 20 nu- cleotides. We then used HybPiper version 1.3 (Johnson et al., 2016) to extract and sort ...
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EvalMSA: a Program to Evaluate Multiple Sequence Alignments and Detect Outliers
... Multiple sequence alignments (MSAs) are essential instruments for prediction of protein structure and function, phylogenetic inference, and other tasks related to sequence ...such ...
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Detecting species-site dependencies in large multiple sequence alignments
... Neither sequence-based nor site-based methods are on their own able to detect any recombination ...event. Phylogenetic algorithms average over the length of the alignment, rightfully discarding the subtle ...
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MUTATIONS AND SEQUENCE ALIGNMENTS
... pairwise sequence alignments contained in T (! [8] , [1010]), T (! [8] , [0110]) and T (! [8] , [1100]) that encode multiple sequence alignments between the sequences of Anne, Bob and ...
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Analysis of Chimpanzee History Based on Genome Sequence Alignments
... multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a ...macaque. Analysis provides a ...
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Techniques for Multiple Sequence Alignments
... Pro reprezentaci biologických sekvencí se používá třída Sequence . Ta obsahuje několik vlastností: typ sekvence (sekvence nukleotidů, aminokyselin), jednoznačný identifikátor sekvence, volitelně popis obsahu ...
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Multiple Sequence Alignments in Linguistics
... multiple sequence align- ments of X-SAMPA word transcriptions we modi- fied ALPHAMALIG slightly so it could work with the tokens that consist of more than one symbol, such as ["e], ["e:] and ...
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
... Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads ...
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Multilocus Sequence Typing and Phylogenetic Analysis of Propionibacterium acnes
... the phylogenetic tree. A detailed analysis of each of the 76 genes by tree construction revealed a mosaic pattern in the strains HL025PA1, SK187, and ...
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A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis
... The first pattern can be seen in several parts of the tree. In the Boletales (Fig. 2a, all groups) the wood-decaying species of the Coniophoraceae (groups 3 and 4) and Paxillaceae (group 3) appear to be the close ...
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A tool for assessing the quality of multiple sequence alignments
... sumy párů Z hlediska sloupcového skóre Z hlediska Z-skóre Z hlediska entropie Nejvhodnější celkově RV11 Muscle Kalign Mafft Mafft T-Coffee Muscle Muscle Mafft Matlab [r] ...
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