search

OpenTreeOfLife / phylografter

web2py app for tree store and grafting
Other
6 stars 4 forks source link

treebase import tree labels #85

Closed blackrim closed 11 years ago

blackrim commented 11 years ago

Treebase import seems to be randomizing the names of the trees on import. For example http://www.reelab.net/phylografter/study/view/2044 has the wrong tree labels for the newick trees.

rhr commented 11 years ago

What do you mean by wrong, and how can you tell? It would help if you could point to a specific tree and tip, thanks.

It does seem to the case that the trees in the NexML document do not match exactly the trees shown in the figures, but that's not a phylografter issue.

On Wed, Oct 9, 2013 at 1:26 PM, Stephen Smith notifications@github.comwrote:

Treebase import seems to be randomizing the names of the trees on import. For example http://www.reelab.net/phylografter/study/view/2044 has the wrong tree labels for the newick trees.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/85 .

blackrim commented 11 years ago

Yeah, it isn't that the species labels are wrong (maybe they are but that isn't the issue). If you look at the "all genes" tree from phylografter and compare it to the all genes from treebase (Tr61313) you will see that Triphysaria pusilla is sister to some Castilleja (this is phylografter). In the Tr61313 (all genes from treebase) it goes like (Triphysaria_floribunda,Triphysaria_pusilla). So something is different here. It appears that the tree that is "all genes" in phylografter is actually the phyA 112 tree from Treebase based on sharing this relationship (Triphysaria_pusilla:0.020768107312199288,(Castilleja_rubicundula:0.021928846684613472,Castilleja_tenuis:0.019600581062418986):0.0022622862476955143).

On Wed, Oct 9, 2013 at 3:56 PM, Rick Ree notifications@github.com wrote:

What do you mean by wrong, and how can you tell? It would help if you could point to a specific tree and tip, thanks.

It does seem to the case that the trees in the NexML document do not match exactly the trees shown in the figures, but that's not a phylografter issue.

On Wed, Oct 9, 2013 at 1:26 PM, Stephen Smith notifications@github.comwrote:

Treebase import seems to be randomizing the names of the trees on import. For example http://www.reelab.net/phylografter/study/view/2044 has the wrong tree labels for the newick trees.

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/phylografter/issues/85> .

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/85#issuecomment-26003043 .

rhr commented 11 years ago

This is a user error. The tree labeled 'all genes' is actually treebase tree Tr61315 (PhyA 112).

On Wed, Oct 9, 2013 at 3:06 PM, Stephen Smith notifications@github.comwrote:

Yeah, it isn't that the species labels are wrong (maybe they are but that isn't the issue). If you look at the "all genes" tree from phylografter and compare it to the all genes from treebase (Tr61313) you will see that Triphysaria pusilla is sister to some Castilleja (this is phylografter). In the Tr61313 (all genes from treebase) it goes like (Triphysaria_floribunda,Triphysaria_pusilla). So something is different here. It appears that the tree that is "all genes" in phylografter is actually the phyA 112 tree from Treebase based on sharing this relationship (Triphysaria_pusilla:0.020768107312199288,(Castilleja_rubicundula:0.021928846684613472,Castilleja_tenuis:0.019600581062418986):0.0022622862476955143).

On Wed, Oct 9, 2013 at 3:56 PM, Rick Ree notifications@github.com wrote:

What do you mean by wrong, and how can you tell? It would help if you could point to a specific tree and tip, thanks.

It does seem to the case that the trees in the NexML document do not match exactly the trees shown in the figures, but that's not a phylografter issue.

On Wed, Oct 9, 2013 at 1:26 PM, Stephen Smith notifications@github.comwrote:

Treebase import seems to be randomizing the names of the trees on import. For example http://www.reelab.net/phylografter/study/view/2044 has the wrong tree labels for the newick trees.

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/phylografter/issues/85> .

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/phylografter/issues/85#issuecomment-26003043>

.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/85#issuecomment-26003859 .

rhr commented 11 years ago

I fixed the tree labels for study 2044.