{"issue":{"state":"closed","pull_request":{"diff_url":null,"html_url":null,"patch_url":null},"user":{"avatar_url":"https://secure.gravatar.com/avatar/21e9f9871d5d84b9eb38ee5b170e375e?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"21e9f9871d5d84b9eb38ee5b170e375e","url":"https://api.github.com/users/smirarab","login":"smirarab","id":826296},"milestone":null,"assignee":null,"labels":[],"updated_at":"2011-11-02T23:08:36Z","closed_at":"2011-11-02T23:08:36Z","comments":1,"url":"https://api.github.com/repos/sate-dev/sate-core/issues/5","body":"For some reason sequences appear twice in my output alignment, one time with the correct sequence name, and other time with everything translated to lower case. So, if I have 50 sequences, I see 100 sequences in the output alignment. \r\n\r\nIt seems that the error is just in outputting the alignment because 1- the output tree is fine, 2- the input alignment to the RAxML in final step in the temp directory is fine. \r\n\r\nI will send out example test cases separately (sorry I cannot post my datasets here)!","html_url":"https://github.com/sate-dev/sate-core/issues/5","number":5,"title":"Sequences appear twice in the Alignment output file","id":2127225,"created_at":"2011-11-02T22:13:07Z"},"action":"closed"}