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32 lines
1.3 KiB
Text
32 lines
1.3 KiB
Text
PRANK: Probabilistic Alignment Kit
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PRANK is a probabilistic multiple alignment program for DNA, codon and
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amino-acid sequences. It is based on a novel algorithm that treats
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insertions correctly and avoids over-estimation of the number of
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deletion events.
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In addition, PRANK borrows ideas from maximum likelihood (ML) methods
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used in phylogenetics and correctly takes into account the evolutionary
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distances between sequences.
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Lastly, PRANK allows for defining a potential structure for sequences to
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be aligned and then, simultaneously with the alignment, predicts the
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locations of structural units in the sequences.
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NOTE!
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The dependencies listed in the REQUIRED field are not needed for
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building PRANK. They are, however, highly recommended for the complete
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functionality of the program:
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1) Progressive alignment requires a guide tree. If no tree is provided,
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PRANK constructs one by calling MAFFT to make a quick alignment and
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infers an NJ tree from the evolutionary distances based on that.
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2) The standard PRANK algorithm is based on an exhaustive search of the
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best pairwise solution. PRANK uses Exonerate to anchor the pairwise
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alignments and thus speed up the process.
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3) To improve the ancestral reconstruction, PRANK uses BppAncestor from
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the BppSuite.
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NOTE 2: This will not build on a 32bit system.
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