User: jhc
jhc • 2.8k
- Reputation:
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- Location:
- Spain
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- jhcepas
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- 1 month, 1 week ago
- Joined:
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Posts by jhc
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0
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243
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... not sure I understood the question, but hope the following points help:
- `resolves_politomies()` does not return a new tree, it modifies the tree inplace.
- the `tree.standardize()` function would be useful to remove one child nodes
- to export a tree in newick, use `tree.write()` not `tree.g ...
written 4 months ago by
jhc • 2.8k
0
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1
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648
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1
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... you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/ ...
written 16 months ago by
jhc • 2.8k
1
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639
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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 18 months ago by
jhc • 2.8k
2
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0
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639
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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 18 months ago by
jhc • 2.8k
1
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0
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395
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0
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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 19 months ago by
jhc • 2.8k
5
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1
answer
809
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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 21 months ago by
jhc • 2.8k
0
votes
2
answers
830
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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 22 months ago by
jhc • 2.8k
1
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0
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951
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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 22 months ago by
jhc • 2.8k
0
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2
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1.5k
views
2
answers
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 2.3 years ago by
jhc • 2.8k
0
votes
1
answer
947
views
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 2.4 years ago by
jhc • 2.8k
Latest awards to jhc
Appreciated
13 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Popular Question
18 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
20 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Scholar
21 months ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated
21 months ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Scholar
21 months ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
2.5 years 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
2.6 years 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
2.6 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher
2.7 years ago,
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For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
2.7 years 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
3.1 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
3.1 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
3.1 years ago,
created 100 posts.
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Good Answer
3.4 years ago,
created an answer that was upvoted at least 5 times.
For A: Parsing A Tree File
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