Protein sequence alignments and phylogenetic trees
DendroBlast: approximate phylogenetic trees in the absence of multiple sequence alignments
... simulated protein sequence alignments from a previous analysis comprising 308 simulated multiple sequence alignments ...These alignments were simulated on realistic tree ...
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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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Protein sequence and structure alignments within one framework
... Results Classification in general Fragment classifications were attempted for pure sequence, pure structure and combined sequence+struc- ture and for fragment lengths up to k = 6. Larger values of k may be ...
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Core column prediction for protein multiple sequence alignments
... Results: We develop for the first time a predictor of column coreness for protein multiple sequence alignments. This allows us to predict which columns of a computed alignment are core, and hence ...
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
... the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered ...on alignments, the methodology set forth here will guide the development of better filtering ...
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DivA: detection of non homologous and very divergent regions in protein sequence alignments
... Conclusions The present method was developed to solve the subjective and time-consuming problem of manual annotation and identification of incorrect gene annotation in genomic pro- jects with phylogenomic studies. It ...
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Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
... Patrick Kück* 1 , Karen Meusemann 1 , Johannes Dambach 1 , Birthe Thormann 1 , Björn M von Reumont 1 , Johann W Wägele 1 and Bernhard Misof 2 Abstract Background: Methods of alignment masking, which refers to the ...
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Visualization of Phylogenetic Trees and Metadata
... A phylogenetic tree can now be reconstructed Using the multiple sequence alignment created in the previous ...the Alignments and Trees section of the ...constructs trees using one of ...
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Data mining for important amino acid residues in multiple sequence alignments and protein structures
... or protein stability for each residue-position of a ...multiple sequence alignment and a 3D structure of one protein in PDB ...seven sequence- based and two structure-based features, each of ...
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Progressive Multiple Sequence Alignments from Triplets
... and alignments of various alignments tools from BAliBASE [Thompson et ...each sequence set as a measurement for alignment quality, Figure ...local sequence context or properties of partial ...
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Phylogenetic assessment of alignments reveals neglected tree signal in gaps
... of trees rather than protein structure to assess alignments is advantageous in that it more closely fits a common application of alignments, it is not restricted to the relatively small and ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... for protein se- quence ...first sequence alignment viewer and editor implemented in Java, a platform independent programming language allowing graphical user interfaces (GUIs) to run on any operating ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visu- alize conservation across protein families as well as unusual ...
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Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks
... Here, we present a consistent way to use pathogen genetic sequence data in transmission tree reconstruction, by simultaneously estimating the phylogenetic tree of the pathogens. This requires inclusion of a ...
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Distance based Phylogenetic Trees with Bootstrapping
... with phylogenetic inference is that the data which is in a single set is of finite ...pairwise alignments are also built ...on phylogenetic trees that are ...
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SearchTree: Mining robust phylogenetic trees
... and sequence ids in data base be |T axonIds| and |SequenceIds| ...each sequence is reverse mapped to only one taxon, storing the taxon-sequence mapping in a simple grouped like fashion makes sense ...
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Parallel computation of phylogenetic consensus trees
... molecular sequence data, predominantly driven by novel wet-lab sequencing ...of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is ...
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SeqTools: visual tools for manual analysis of sequence alignments
... missing/misaligned sequence and to identify splice sites and polyA sites and ...identify sequence that is not represented (or is misrepresented) and to quickly compare annotated gene models with ...
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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 alignments, ...
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Noisy: Identification of problematic columns in multiple sequence alignments
... of protein-coding ...decreasing sequence length, it is impor- tant not to remove too many sites from an align- ...of protein-coding genes can well be informative and should not be just discarded as ...
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