{"action":"closed","issue":{"url":"https://api.github.com/repos/brettc/partitionfinder/issues/107","repository_url":"https://api.github.com/repos/brettc/partitionfinder","labels_url":"https://api.github.com/repos/brettc/partitionfinder/issues/107/labels{/name}","comments_url":"https://api.github.com/repos/brettc/partitionfinder/issues/107/comments","events_url":"https://api.github.com/repos/brettc/partitionfinder/issues/107/events","html_url":"https://github.com/brettc/partitionfinder/issues/107","id":158169994,"number":107,"title":"Fix RAxML warning message about GTR+G and GTR+I+G","user":{"login":"pbfrandsen","id":1823345,"avatar_url":"https://avatars.githubusercontent.com/u/1823345?v=3","gravatar_id":"","url":"https://api.github.com/users/pbfrandsen","html_url":"https://github.com/pbfrandsen","followers_url":"https://api.github.com/users/pbfrandsen/followers","following_url":"https://api.github.com/users/pbfrandsen/following{/other_user}","gists_url":"https://api.github.com/users/pbfrandsen/gists{/gist_id}","starred_url":"https://api.github.com/users/pbfrandsen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbfrandsen/subscriptions","organizations_url":"https://api.github.com/users/pbfrandsen/orgs","repos_url":"https://api.github.com/users/pbfrandsen/repos","events_url":"https://api.github.com/users/pbfrandsen/events{/privacy}","received_events_url":"https://api.github.com/users/pbfrandsen/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-06-02T15:28:34Z","updated_at":"2016-06-02T21:41:01Z","closed_at":"2016-06-02T21:41:01Z","body":"A user at SI was confused by the following message because his partitioning scheme, included GTR models without a model of rate heterogeneity and because the examples referred to protein analyses (his were nt):\r\n\r\n> \"Warning: RAxML allows for only a single model of rate heterogeneity in partitioned analyses. I.e. all partitions must be assigned either a +G model or a +I+G model. If the best models for your datasetcontain both types of model, you will need to choose an appropriate rate heterogeneity model when you run RAxML. This is specified through the command line to RAxML. To rigorously choose the best model, run two further PF analyses (these will be fast), fixing the partitioning scheme to this scheme and 'search=user;', in both. In one run, use only +I+G models ('models = all_protein_gammaI'); in the next, use only +G models ('models = all_protein_gamma;''). Choose the scheme with the lowest AIC/AICc/BIC score. Note that these re-runs will be quick!\"\r\n\r\nWe should add that RAxML supports GTR and put something in there so that users will know that it applies to nucleotide data as well."}}
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