Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
نویسندگان
چکیده
منابع مشابه
Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignmen...
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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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In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, bot...
متن کاملImproving the Efficiency of Multiple Sequence Alignment by Genetic Algorithms
Multiple alignments of biological nucleic acid sequences are one of the most commonly used techniques in sequence analysis. These techniques demand a big computational load. We present a Genetic Algorithms (GA) that optimizes an objective function that is a measure of alignment quality (distance). Each individual in the population represents (in an efficient way) some underlying operations on t...
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ژورنال
عنوان ژورنال: Evolutionary Bioinformatics
سال: 2014
ISSN: 1176-9343,1176-9343
DOI: 10.4137/ebo.s19199