User: jhc
jhc • 2.8k
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Posts by jhc
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... you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/ ...
written 6 months ago by
jhc • 2.8k
1
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396
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... The CBGP is seeking for outstanding candidates for postdoctoral researcher positions in the CBGP Computational-Systems Biology and Genomics Program (CSBGP).
The Center for Plant Biotechnology and Genomics (CBGP), a joint research institute from Universidad Politécnica de Madrid (UPM) and the Instit ...
written 8 months ago by
jhc • 2.8k
2
votes
0
answers
395
views
0
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Job:
Junior Group Leader position in Computational Systems Biology and Genomics at CBGP (Madrid, Spain
... **CBGP is seeking** for a new Group Leader to cover one of the following research areas:
Genomic Assisted Breeding
Computational Structural Biology
Synthetic and Systems Biology
We are looking for a highly motivated and productive scientist at Junior level to initiate a recognized research group i ...
written 8 months ago by
jhc • 2.8k
1
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0
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237
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... not possible at the moment. It would require a very small change in the code increasing the max length from 15 to anything else: https://github.com/etetoolkit/ete/blob/da6a23ae7adbe98be26a232a29fd90af3a66b0b5/ete3/tools/ete_compare.py#L185
...
written 9 months ago by
jhc • 2.8k
5
votes
1
answer
511
views
1
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... try something like this:
from ete3 import Tree
def is_ultrametric(tree):
last_distance = None
distance = 0
for post, node in tree.iter_prepostorder():
if post:
distance -= node.dist
else:
if not node.is ...
written 11 months ago by
jhc • 2.8k
0
votes
2
answers
450
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2
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... If you have the NCBI taxid code for each species, yes, it is possible to do it with ETE.
Check this part of the documentation:
http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html
http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 12 months ago by
jhc • 2.8k
1
vote
0
answers
703
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0
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Job:
3 positions in Computational Genomics at CBGP in Madrid, Spain. (Postdoc, Predoc and Technician)
... 3 positions are available in the Computational Evolutionary Genomics group at CBGP (Madrid, Spain):
1. Research technician to work on bioinformatics tools such as [ETE][1]
toolkit or [eggNOG][2]. **(closed)**
2. PhD in comparative metagenomics via INPhiNIT program **(closed)**
3. Postdoc in ...
written 12 months ago by
jhc • 2.8k
0
votes
2
answers
1.1k
views
2
answers
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 18 months ago by
jhc • 2.8k
0
votes
1
answer
636
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1
answers
Answer:
A: EggNOG 4.5 database
... the databases bact_50 and bactNOG are not exactly the same. The first (bact_50) includes all bactNOG groups plus all OGs in children taxonomic levels for bactNOGs including more than 50 sequences (this is to increase HMM resolution in groups that are too large). Something similar occurs with euk vs ...
written 19 months ago by
jhc • 2.8k
1
vote
3
answers
1.0k
views
3
answers
... for NCBI trees, check [ete-ncbiquery][1]
[1]: http://etetoolkit.org/documentation/ete-ncbiquery/ ...
written 20 months ago by
jhc • 2.8k
Latest awards to jhc
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Popular Question
8 months ago,
created a question with more than 1,000 views.
For ETE build: from sequences to phylogenetic trees with just a single command line.
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Scholar
11 months ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Scholar
11 months ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For ETE build: from sequences to phylogenetic trees with just a single command line.
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher
22 months ago,
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For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher
22 months ago,
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For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar
22 months ago,
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For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Program for searching for a specific partition within a set of phylogenetic tree
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Centurion
2.2 years ago,
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Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
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2.6 years ago,
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For A: How Can I Plot Go Data Using R Or Any Tools?
Good Answer
2.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Parsing A Tree File
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