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Handel (bioinformatics software package)

Handel (bioinformatics software package)

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Handel is a suite of programs for multiple sequence alignment
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...

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Since it is based on a model of DNA sequence evolution
Models of DNA evolution
A number of different Markov models of DNA sequence evolution have been proposed. These substitution models differ in terms of the parameters used to describe the rates at which one nucleotide replaces another during evolution. These models are frequently used in molecular phylogenetic analyses...


that explicitly incorporates insertion and deletion events
Indel
Indel is a molecular biology term that has different definitions in different fields:*In evolutionary studies, indel is used to mean an insertion or a deletion and indels simply refers to the mutation class that includes both insertions, deletions, and the combination thereof, including insertion...

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it effectively doubles as a program for ancestral sequence reconstruction
Ancestral Reconstruction
- Trait reconstruction :Ancestral reconstruction is widely use to infer the ecological, phenotypic, or biogeographic traits associated with ancestral nodes in a phylogenetic tree...

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The theory underpinning Handel is based on the finite state transducer
Finite state transducer
A finite state transducer is a finite state machine with two tapes: an input tape and an output tape. This contrasts with an ordinary finite state automaton , which has a single tape.-Overview:...

, a concept borrowed from computational linguistics.

Handel can be downloaded as part of the DART software package. It accepts input files in Stockholm format.

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