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I'll remove this in the next commit.","created_at":"2016-08-17T02:16:32Z","updated_at":"2016-08-17T02:16:32Z","html_url":"https://github.com/BioJulia/Bio.jl/pull/258#discussion_r75053468","pull_request_url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/258","_links":{"self":{"href":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/comments/75053468"},"html":{"href":"https://github.com/BioJulia/Bio.jl/pull/258#discussion_r75053468"},"pull_request":{"href":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/258"}}},"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/258","id":81317281,"html_url":"https://github.com/BioJulia/Bio.jl/pull/258","diff_url":"https://github.com/BioJulia/Bio.jl/pull/258.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/258.patch","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/258","number":258,"state":"open","locked":false,"title":"Mutation counting","user":{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars.githubusercontent.com/u/3399309?v=3","gravatar_id":"","url":"https://api.github.com/users/Ward9250","html_url":"https://github.com/Ward9250","followers_url":"https://api.github.com/users/Ward9250/followers","following_url":"https://api.github.com/users/Ward9250/following{/other_user}","gists_url":"https://api.github.com/users/Ward9250/gists{/gist_id}","starred_url":"https://api.github.com/users/Ward9250/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ward9250/subscriptions","organizations_url":"https://api.github.com/users/Ward9250/orgs","repos_url":"https://api.github.com/users/Ward9250/repos","events_url":"https://api.github.com/users/Ward9250/events{/privacy}","received_events_url":"https://api.github.com/users/Ward9250/received_events","type":"User","site_admin":false},"body":"Implementation of counting of different types of mutations.\r\n\r\nA nessecery precursor to the evolutionary distance PR, but sizable enough that I've separated into its own PR.\r\n\r\nAt first (in this PR), only two kinds of mutation counting will be implemented: counting different nucleotides, and counting the number of transitions and number of transversions.\r\n\r\nThe count_mutations method uses a strict ambiguity test, which discounts a site completely from the computation if either nucleotide is uncertain or a gap i.e. ambiguity codes.\r\n\r\nI tried experimenting (hence all the commits!) with making use of all symbols including ambiguities as sometimes it is possible to tell if two ambiguous sites, are different or are say a transition/transversion despite their ambiguity. However because of the complexity of doing this, plus the bias it could introduce in downstream analysis if applied uncritically (for example you can always detect more mutated sites with ambiguity codes, than you can conserved sites), it is not worth doing - if a sequence were that ambiguous, maybe you need better sequence data in the first place 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