{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/157","labels_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/157/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/157/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/157/events","html_url":"https://github.com/OpenTreeOfLife/treemachine/issues/157","id":56118899,"number":157,"title":"synthesis issue: only using mrca taxa from an edge (\"relationship\" in neo4j lingo) rather than node","user":{"login":"mtholder","id":136067,"avatar_url":"https://avatars.githubusercontent.com/u/136067?v=3","gravatar_id":"","url":"https://api.github.com/users/mtholder","html_url":"https://github.com/mtholder","followers_url":"https://api.github.com/users/mtholder/followers","following_url":"https://api.github.com/users/mtholder/following{/other_user}","gists_url":"https://api.github.com/users/mtholder/gists{/gist_id}","starred_url":"https://api.github.com/users/mtholder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtholder/subscriptions","organizations_url":"https://api.github.com/users/mtholder/orgs","repos_url":"https://api.github.com/users/mtholder/repos","events_url":"https://api.github.com/users/mtholder/events{/privacy}","received_events_url":"https://api.github.com/users/mtholder/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":20,"created_at":"2015-01-31T09:12:18Z","updated_at":"2015-02-01T12:41:10Z","closed_at":null,"body":"I just pushed https://github.com/OpenTreeOfLife/treemachine/tree/issue-157 with some very simple examples to help debug https://github.com/OpenTreeOfLife/treemachine/issues/156 \r\n\r\nBut I'm not getting the tree that one would hope for when I run:\r\n\r\n    $ run-simpleprob-example-diff-order-synth.sh\r\n\r\nand look a the result in `simpleprob-diff-order-out/synth.tre`\r\n\r\nThe inputs have not conflict and there is no evidence of non-monophyly of the taxa. So I would hope that the synthesis would return the tree in `simpleprob/expected.tre`\r\n\r\nThere is a (**very**) good chance that I'm just running treemachine incorrectly. If @blackrim @josephwb or @chinchliff  could take a look at  `run-simpleprob-example-diff-order-synth.sh` I would really appreciate it.\r\n\r\nI pulled and built jade and ot-base before pulling and building treemachine."},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/comments/72363221","html_url":"https://github.com/OpenTreeOfLife/treemachine/issues/157#issuecomment-72363221","issue_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/157","id":72363221,"user":{"login":"blackrim","id":160553,"avatar_url":"https://avatars.githubusercontent.com/u/160553?v=3","gravatar_id":"","url":"https://api.github.com/users/blackrim","html_url":"https://github.com/blackrim","followers_url":"https://api.github.com/users/blackrim/followers","following_url":"https://api.github.com/users/blackrim/following{/other_user}","gists_url":"https://api.github.com/users/blackrim/gists{/gist_id}","starred_url":"https://api.github.com/users/blackrim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blackrim/subscriptions","organizations_url":"https://api.github.com/users/blackrim/orgs","repos_url":"https://api.github.com/users/blackrim/repos","events_url":"https://api.github.com/users/blackrim/events{/privacy}","received_events_url":"https://api.github.com/users/blackrim/received_events","type":"User","site_admin":false},"created_at":"2015-02-01T12:41:10Z","updated_at":"2015-02-01T12:41:10Z","body":"The branch (and bound) method that I mentioned that addresses this problem\r\nis in there both in the conflict resolution folder and explorer in graph\r\nsynthesis function. I am tracking down the main so I can do your example\r\nand will push that. However it uses very old code and doesn't seem to have\r\nbeen brought up to some of the newer classes that Cody wrote.  I don't\r\nthink it is worth it to do that and instead probably best to write some new\r\nones including of the pseudo code you had (if you haven't already done that)\r\nOn Feb 1, 2015 6:55 AM, \"Stephen Smith\" <blackrim@gmail.com> wrote:\r\n\r\n> Cool, well check out in a bit.  Also, just noting here something I\r\n> mentioned in the other issue.  We constructed a branch and bound ( though\r\n> really mostly branch) synth that also is discussed in the paper and deals\r\n> with this issue nicely.  It simply doesn't scale well with the many\r\n> millions nodes.  It is in the code and can be switched on however for the\r\n> big tree perhaps your solution will work better.\r\n> On Feb 1, 2015 6:16 AM, \"Mark T. Holder\" <notifications@github.com> wrote:\r\n>\r\n>> I should have mentioned that I tested this change on the\r\n>> RankNodeDesResolutionMethod branch that I just pushed.\r\n>>\r\n>> —\r\n>> Reply to this email directly or view it on GitHub\r\n>> <https://github.com/OpenTreeOfLife/treemachine/issues/157#issuecomment-72360731>\r\n>> .\r\n>>\r\n>"}}