{"action":"created","issue":{"url":"https://api.github.com/repos/naturalis/supersmart/issues/47","labels_url":"https://api.github.com/repos/naturalis/supersmart/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/naturalis/supersmart/issues/47/comments","events_url":"https://api.github.com/repos/naturalis/supersmart/issues/47/events","html_url":"https://github.com/naturalis/supersmart/issues/47","id":60677081,"number":47,"title":"option to include all species in supermatrix","user":{"login":"hettling","id":4069510,"avatar_url":"https://avatars.githubusercontent.com/u/4069510?v=3","gravatar_id":"","url":"https://api.github.com/users/hettling","html_url":"https://github.com/hettling","followers_url":"https://api.github.com/users/hettling/followers","following_url":"https://api.github.com/users/hettling/following{/other_user}","gists_url":"https://api.github.com/users/hettling/gists{/gist_id}","starred_url":"https://api.github.com/users/hettling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hettling/subscriptions","organizations_url":"https://api.github.com/users/hettling/orgs","repos_url":"https://api.github.com/users/hettling/repos","events_url":"https://api.github.com/users/hettling/events{/privacy}","received_events_url":"https://api.github.com/users/hettling/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/naturalis/supersmart/milestones/2","html_url":"https://github.com/naturalis/supersmart/milestones/v2.0","labels_url":"https://api.github.com/repos/naturalis/supersmart/milestones/2/labels","id":1065159,"number":2,"title":"v2.0","description":"Milestone for all the enhancements that are deferred till after v1.0. For now this may become a gathering place for all blue sky thinking about things such as:\r\n* automatic harvesting of fossil calibrations through a web service API: this functionality simply doesn't exist yet so there is no client for us to write.\r\n* recursive inference: this constitutes a pretty big enhancement/rewrite which we don't yet need for the scale at which we are working now, but it'll become important later down the line.\r\n* inclusion of NGS data: too much work for now, defer.","creator":{"login":"rvosa","id":106490,"avatar_url":"https://avatars.githubusercontent.com/u/106490?v=3","gravatar_id":"","url":"https://api.github.com/users/rvosa","html_url":"https://github.com/rvosa","followers_url":"https://api.github.com/users/rvosa/followers","following_url":"https://api.github.com/users/rvosa/following{/other_user}","gists_url":"https://api.github.com/users/rvosa/gists{/gist_id}","starred_url":"https://api.github.com/users/rvosa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rvosa/subscriptions","organizations_url":"https://api.github.com/users/rvosa/orgs","repos_url":"https://api.github.com/users/rvosa/repos","events_url":"https://api.github.com/users/rvosa/events{/privacy}","received_events_url":"https://api.github.com/users/rvosa/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":0,"state":"open","created_at":"2015-04-13T14:26:30Z","updated_at":"2015-04-13T14:41:16Z","due_on":null,"closed_at":null},"comments":1,"created_at":"2015-03-11T15:32:30Z","updated_at":"2015-04-13T14:41:19Z","closed_at":null,"body":"It would be desirable to give the user the option to include all species from the taxafile into the supermatrix. Especially if a single genus is chosen for analysis, a stepwise inference does not make sense. The user could then export the supermatrix in the desired format (fasta, phylip, nexus, ...) and do a single inference with his favorite inference tool."},"comment":{"url":"https://api.github.com/repos/naturalis/supersmart/issues/comments/92385379","html_url":"https://github.com/naturalis/supersmart/issues/47#issuecomment-92385379","issue_url":"https://api.github.com/repos/naturalis/supersmart/issues/47","id":92385379,"user":{"login":"rvosa","id":106490,"avatar_url":"https://avatars.githubusercontent.com/u/106490?v=3","gravatar_id":"","url":"https://api.github.com/users/rvosa","html_url":"https://github.com/rvosa","followers_url":"https://api.github.com/users/rvosa/followers","following_url":"https://api.github.com/users/rvosa/following{/other_user}","gists_url":"https://api.github.com/users/rvosa/gists{/gist_id}","starred_url":"https://api.github.com/users/rvosa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rvosa/subscriptions","organizations_url":"https://api.github.com/users/rvosa/orgs","repos_url":"https://api.github.com/users/rvosa/repos","events_url":"https://api.github.com/users/rvosa/events{/privacy}","received_events_url":"https://api.github.com/users/rvosa/received_events","type":"User","site_admin":false},"created_at":"2015-04-13T14:41:19Z","updated_at":"2015-04-13T14:41:19Z","body":"This is not so important. We don't really intend SUPERSMART to infer the relationships within a single genus. We nonetheless deal with this issue sometimes (especially for testing) but it's not important enough to worry about for v1.0."}}