Multiple Sequence Alignments, Trees, and
DendroBlast: approximate phylogenetic trees in the absence of multiple sequence alignments
... of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred ...simulated sequence data we demonstrate that this method produces ...
11
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... as sequence retrieval, computation of alignments and communication with ...of sequence by drag-and-drop, and residue annotation as well as links to 3D visualization and sequence ...that ...
10
Noisy: Identification of problematic columns in multiple sequence alignments
... The analysis of several published data sets shows that removal of randomized sites consistently leads to more stable trees, irrespective of the method used for phylogeny reconstruction (neighbor joining, maximum ...
10
Noisy: Identification of problematic columns in multiple sequence alignments
... 100.000 trees at ran- dom from all possible tree topologies (replacements ...for trees — resulting, in our case, from neighbor join- ing ...joining trees computed using PAUP ...
11
Detecting species-site dependencies in large multiple sequence alignments
... INTRODUCTION Multiple sequence alignments (MSAs) are high dimen- sional discrete datasets, which play a prominent role in ...evolutionary trees, for ...general sequence clustering ...
10
Sequence embedding for fast construction of guide trees for multiple sequence alignment
... than sequence distances, and this allows us to rapidly generate a distance matrix δ (F(x), F(y)) from a set of embedded ...the sequence vectors can be clustered using an alternative clustering method such ...
11
Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
... Results: ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap ...
12
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
... 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 ...on alignments, the methodology ...
14
ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection
... DNA sequence polymorphism ...DNA sequence chromatograms to correct base-calling and sequencing ...individual sequence reads into longer contigs using Phred and Phrap (these are not included in ProSeq ...
18
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees
... guide trees for normally related sequences PnpProbs uses an adaptive approach to generating guide trees for normally related ...resulting alignments, which is one of the most commonly used ...
11
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 ...
13
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 ...
55
Multiple Sequence Alignments in Linguistics
... perform 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 ...
8
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] ...
69
Progressive Multiple Sequence Alignments from Triplets
... Progressive sequence alignments, while computationally efficient, suffer from two major ...score-equivalent alignments among which the algorithm chooses one by means of a pragmatic rule ...
19
Progressive multiple sequence alignments from triplets
... Instead of a phylogenetic tree aln3nn uses a phylogenetic network to calculate the alignment order. The network is constructed using the Neighbor-Net (Nnet) approach, a distance based clustering algorithm that can be ...
12
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... a sequence and the se- quence itself — all sequences must be ...the sequence should be doti- fied and whether repeated residues should be coloured; (iv) whether a consensus sequence should be ...
6
SVM-based Automatic Annotation of Multiple Sequence Alignments
... Comparison with existing editing tools had been carried out and revealed this method can facilitate the process of multiple alignments annotation. It is stable for both of RBF parameters (c & gamma). This ...
8
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 ...
16
OD-seq: outlier detection in multiple sequence alignments
... Outlier detection is a well studied field in computer sci- ence and has been applied to many different fields such as credit card, insurance and tax fraud detection, intru- sion detection for cyber security, fault ...
11