Probabilistic reconstruction of ancestral protein sequences
نویسندگان
چکیده
منابع مشابه
FastML: a web server for probabilistic reconstruction of ancestral sequences
Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. F...
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This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate...
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The problem of ancestral sequence reconstruction is the statistical inference of sequences that correspond to internal nodes in a phylgenetic tree [1]. Joint reconstruction is the task of seeking the most likely set of ancestral states corresponding to all the ancestral taxa, while marginal reconstruction aims at inferring the sequence in a specific internal node. In simple probabilistic models...
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A challenging task in computational biology is the reconstruction of genomic sequences of extinct ancestors, given the phylogenetic tree and the sequences at the leafs. This task is best solved by calculating the most likely estimate of the ancestral sequences, along with the most likely edge lengths. We deal with this problem and also the variant in which the phylogenetic tree in addition to t...
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An evolutionary configuration (EC) is a set of aligned sequences of characters (possibly representing amino acids, DNA, RNA or natural language). We define the probability of an EC, based on a given phylogenetic tree and give an algorithm to compute this probability efficiently. From these probabilities, we can compute the most likely sequence at any place in the phylogenetic tree, or its proba...
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ژورنال
عنوان ژورنال: Journal of Molecular Evolution
سال: 1996
ISSN: 0022-2844,1432-1432
DOI: 10.1007/bf02198858