Question: Reduced versions of the 23MB tree by scripts?
0
gravatar for monstercolorfun
4.0 years ago by
monstercolorfun10 wrote:

I am working on a school biology program using alot of 3D and physx to represent trees, and I also have to write the tree parsing algorithms so it's quite a steep learning process in phylogeny trees.

the first tree I found was 1.79MB and formatted with branch length: 

8):3.5):0.0,(Boselaphus_tragocamelus:6.716975,Tetracerus_quadricornis:6.716975):10.583025):

and now I have the 23MB version which is formatted:

(Azaera_nodoses_ott3154881,Azaera_lophophora_ott3157572,Azaera_squalidella_ott3154879,Azaera_muciella_ott3157571)Azaera_ott3154880,

I am only interested in species for which there could be a photo online, so I can delete all the species of type:

Azaera_ott3154880 ?

And then, there is also SP_... I can get rid of all the SP ones because they are not practical for a amateur biology research?

Are there other types of species nomenclatures other than ott and SP  that i should take away from the project to make it easier?

Then i just have to rewrite the parser to use _ott as a species demarker and ) as a node demarker, are there some simplified reformatted versions of the tree available, can someone reccommend me a program where by i can take out everything that isnt binomial nomenclature and save as a .NWK file?

If Gaia time permits can you even write a new tree for me and upload it as a new resource for general use for the internet keeping only binomial named species?

Thanks!

 

 

 

ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 4.0 years ago by monstercolorfun10

I WOULD BE VERY GRATEFUL IF SOMEONE COULD SAVE ME 3 TREES, ANIMALAE, PLANTAE, AND FUNGHI, INTO 3 NEWICK FILES AND UPLOAD THEM SOME PLACE? PLEASE

ADD REPLYlink written 3.9 years ago by monstercolorfun10
0
gravatar for jhc
4.0 years ago by
jhc2.8k
Spain
jhc2.8k wrote:

There are many, check ETE toolkit, Biopython, Bio::Phylo, Dendropy...

ADD COMMENTlink written 4.0 years ago by jhc2.8k

Thankyou jhc, i tried the ones that you mention, they are all for linux, i have managed to install figuetree and it's java so virtual memory problems probably for 2mn species tree. I ll try to find something for win32, will say what happens. thanks.

ADD REPLYlink written 4.0 years ago by monstercolorfun10

I still didn't manage to find a single windows program that can load and edit the open tree of life file. even NotePad++ can't open it. It is 80mb .tre uncompressed. I figure i have to make a code for it using windows C# openstreamreader library.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by monstercolorfun10
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