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Phylo (video game)
''Phylo'' is an experimental video game about multiple sequence alignment optimisation.〔 Developed by the McGill Centre for Bioinformatics, it was originally released as a free Flash game in November 2010. Designed as a game with a purpose, players solve pattern-matching puzzles that represent nucleotide sequences of different phylogenetic taxa to optimize alignments over a computer algorithm. By aligning together each nucleotide sequence, represented as differently coloured blocks, players attempt to create the highest point value score for each set of sequences by matching as many colours as possible and minimizing gaps.
The nucleotide sequences generated by ''Phylo'' are obtained from actual sequence data from the UCSC Genome Browser. High-scoring player alignments are collected as data and sent back to the McGill Centre for Bioinformatics to be further evaluated with a stronger scoring algorithm. Those player alignments that score higher than the current computer-generated score will be re-introduced into the global alignment as an optimization.
==Background==
The goal of multiple sequence alignments in phylogenetics is to determine the most likely nucleotide sequence of each species by comparing the sequences of children species with those of a most recent common ancestor. Producing such an optimal multiple sequence alignment is usually determined with a dynamic programming algorithm that finds the most probable evolutionary outcome by minimizing the number of mutations required. These algorithms generate phylogenetic trees for each nucleotide in a sequence for each species, and determine the genetic sequence for a common ancestor by comparing the trees of the child species. The algorithms then score and sort the completed phylogenetic tree, and the alignment with the maximum parsimony score is determined to be the optimal, and thus most evolutionarily likely, multiple sequence alignment. However, finding such an optimal alignment for a large number of sequences has been determined to be an NP-complete problem.
''Phylo'' uses human-based computation to create an interactive genetic algorithm to solve the multiple sequence alignment problem instead. Generation of the ancestral sequences and parsimony scoring is still computed using a variation of the Fitch algorithm, but ''Phylo'' abstracts the genetic sequences obtained from the UCSC Genome Browser into a pattern-matching game, allowing human players to suggest the most likely alignment rather than algorithmically considering all possible trees.
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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