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| − | Supposing you have already found a template candidate, you need to align it against your target sequence.
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| − | The '''subali''' application let you choose from very different type of algorithms, strategies and parameters.
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| − | Strategy:
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| − | * Sequence to sequence
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| − | * Profile to sequence
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| − | * Profile to profile
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| − | Alignment algorithm:
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| − | * Local
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| − | * Global
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| − | * Freeshift
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| − | Blosum substitution matrix:
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| − | * 62
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| − | * 45
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| − | * 50
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| − | * 80
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| − | Weighting scheme (only for profiles):
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| − | * PSIC (Sunyaev et al., 1999)
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| − | * Henikoff (Henikoff & Henikoff, 1994)
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| − | * SecDivergence (Rychlewski et al., 2000)
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| − | Scoring function (only for profile to profile alignments):
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| − | * Sum of pairs
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| − | ** CrossProduct
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| − | ** LogAverage (Ohsen and Zimmer, 2003; von Ohsen et al., 2003)
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| − | * Dot product
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| − | ** DotPFreq (Wang and Dunbrack, 2004)
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| − | ** DotPOdds (Wang and Dunbrack, 2004)
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| − | * EDistance (Euclidean distance)
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| − | * Pearson (Pietrokovski, 1996)
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| − | * JensenShannon (Yona and Levitt, 2002)
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| − | * Atchley metric
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| − | ** AtchleyDistance (Atchley et al., 2005)
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| − | ** AtchleyCorrelation (Atchley et al., 2005)
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