Phylogenetic automata, pruning, and multiple alignment

Details Phylogenetic automata, pruning, and multiple alignment Phylogenetic automata, pruning, and multiple alignment

2011-03-22

arxiv.org/abs/1103.4347v2

Biology

Quantitative Biology

Populations and Evolution

89 pages: background, informal tutorial, and formal definitions

Scientific paper

We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment. The algorithm makes use of a generalization from probabilistic substitution matrices to weighted finite-state transducers. Our approach may equivalently be viewed as a probabilistic formulation of progressive multiple sequence alignment, using partial-order graphs to represent ensemble profiles of ancestral sequences. We present a hierarchical stochastic approximation technique which makes this algorithm tractable for alignment analyses of reasonable size.

Affiliated with

Also associated with

No associations

Rating

Phylogenetic automata, pruning, and multiple alignment does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Phylogenetic automata, pruning, and multiple alignment, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Phylogenetic automata, pruning, and multiple alignment will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-49622