tag:blogger.com,1999:blog-5286956948868856311.post7940955892684962881..comments2023-06-22T17:21:43.730+02:00Comments on Biodivertido: PhyloBox: A better way to do phylogenetic trees on the webJavier de la Torrehttp://www.blogger.com/profile/03992185734194337802noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-5286956948868856311.post-4156216972483711402010-06-28T21:18:01.698+02:002010-06-28T21:18:01.698+02:00Actually, dblclick in the widget is a bit funny, r...Actually, dblclick in the widget is a bit funny, removing for now.Andrew W Hillhttps://www.blogger.com/profile/04814436364156670727noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-18361246719586841672010-06-28T21:11:55.817+02:002010-06-28T21:11:55.817+02:00Just starting to add some mouse support for tree n...Just starting to add some mouse support for tree navigating. Double-click to zoom, still need to press 'z' to zoom out, also drag the tree to add spin. You may need to refresh this page before the widget picks up the new code.Andrew W Hillhttps://www.blogger.com/profile/04814436364156670727noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-2473903409003735402010-06-26T02:24:06.347+02:002010-06-26T02:24:06.347+02:00@blJOg We now have Newick support. It covers name...@blJOg We now have Newick support. It covers names and branch lengths, but I need to go back and mess with branch lengths plus support values. Enjoy.Andrew W Hillhttps://www.blogger.com/profile/04814436364156670727noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-17033341413365648192010-06-21T19:42:49.294+02:002010-06-21T19:42:49.294+02:00Actually, the branches are perfect rectangles. The...Actually, the branches are perfect rectangles. The wonkyness is the correct mathematical result of placing the branch corners on the same plane as the node and its children. This causes some nodes to have one branch corner at a different depth than its partner. Greater depth must mean different x,y screen position in order to maintain perspective... <br /><br />This technique of maintaining the node-children plane at branch corners seems to be the intuitive approach. However, it makes sense that this wonkyness could be a nuisance when the user wants to see their tree in only 2D. One method to improve would be to just greatly reduce the z-step... which is currently equal to the x-step. ?sanderhttps://www.blogger.com/profile/12565820402395744233noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-21732368568715536192010-06-21T16:27:55.262+02:002010-06-21T16:27:55.262+02:00blJOg, thanks! I'll have a first pass nexus up...blJOg, thanks! I'll have a first pass nexus uploader in a few days, promise. <br />Rod thanks also! Yeah, branches are a bit wonky still just because of the way that we are drawing the reference point in 3D space for the bend. We'll fix it up shortly.<br />Here was our pure 2D version that we are moving towards, http://phylobox.appspot.com/tree/old?k=phylobox-1-0-ecfa61d1-db2b-49a3-9c05-8f4f682e68d9Andrew W Hillhttps://www.blogger.com/profile/04814436364156670727noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-27043372051233400032010-06-21T12:48:18.812+02:002010-06-21T12:48:18.812+02:00@andrewxhill Neat stuff. Is it just me, or are the...@andrewxhill Neat stuff. Is it just me, or are the branches in the example tree image a bit wonky? Is there a reason that they aren't rectangular?Roderic Pagehttps://www.blogger.com/profile/00269598293846172649noreply@blogger.comtag:blogger.com,1999:blog-5286956948868856311.post-55173345547434530812010-06-21T12:18:10.291+02:002010-06-21T12:18:10.291+02:00Great stuff! Like the idea of forking and don'...Great stuff! Like the idea of forking and don't see why researchers wouldn't like it and I think you are right that it would be best not to have an opt-out. <br />I think the idea of commenting on trees, nodes and leaves would be brilliant and to be able to link to those comments would be great. Even better if a user could keep control of his comments to make further edits or even delete it one day.<br />I know that PhyloXML is the new format for phylogenetics but all my trees are in Nexus (it might be an antiquated formatted but all the software I use saves in that format and it is short and simple). I look forward to a Nexus/NeXML -> PhyloJSON converter.blOghttps://www.blogger.com/profile/16883530682517464163noreply@blogger.com