Similarity Score Estimation and Gaps Trimming of Multiple Sequence Alignment for Phylogenetic Tree Analysis
نویسندگان
چکیده
منابع مشابه
Multiple sequence alignment in phylogenetic analysis.
Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since the object of alignment is to create the most efficient statement of initial homology, methods that minimize nonhomology are to be favored. Therefore, among all possible alignments, the one that satisfie...
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Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under differ...
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We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignments of sequences without mutual correlations are found to have scale-invariant statistics. This is the basis for a scaling theory of alignments of correlated sequences. Using a simple Markov model of evolution, we gen...
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We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is ...
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ژورنال
عنوان ژورنال: ECTI Transactions on Computer and Information Technology (ECTI-CIT)
سال: 2017
ISSN: 2286-9131,2286-9131
DOI: 10.37936/ecti-cit.2017112.74783