User: jhc
jhc • 2.9k
- Reputation:
- 2,870
- Status:
- Trusted
- Location:
- Spain
- Twitter:
- jhcepas
- Last seen:
- 9 months ago
- Joined:
- 8 years, 6 months ago
- Email:
- j******@gmail.com
Posts by jhc
<prev
• 120 results •
page 1 of 12 •
next >
0
votes
1
answer
581
views
1
answers
... 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 16 months ago by
jhc • 2.9k
0
votes
1
answer
1.0k
views
1
answers
... you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/ ...
written 2.3 years ago by
jhc • 2.9k
1
vote
0
answers
846
views
0
answers
... 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 2.5 years ago by
jhc • 2.9k
2
votes
0
answers
1.0k
views
0
answers
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 2.5 years ago by
jhc • 2.9k
1
vote
0
answers
511
views
0
answers
... 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 2.5 years ago by
jhc • 2.9k
5
votes
1
answer
1.2k
views
1
answers
... 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 2.7 years ago by
jhc • 2.9k
0
votes
2
answers
1.3k
views
2
answers
... 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 2.8 years ago by
jhc • 2.9k
1
vote
0
answers
1.2k
views
0
answers
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 2.8 years ago by
jhc • 2.9k
0
votes
2
answers
2.0k
views
2
answers
... just the NOG, COGs, arCOGs and KOGs are stable ...
written 3.3 years ago by
jhc • 2.9k
0
votes
1
answer
1.3k
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 3.4 years ago by
jhc • 2.9k
Latest awards to jhc
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Great Question
12 months ago,
created a question with more than 5,000 views.
For When Is Dna Better Choice Than Aminoacids For Multiple Sequence Alignments And Phylogenetic Reconstruction?
Appreciated
2.0 years ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Appreciated
2.2 years ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: etetoolkit, Visualization of phylogenetic trees
Popular Question
2.5 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: etetoolkit, Visualization of phylogenetic trees
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Appreciated
2.7 years ago,
created a post with more than 5 votes.
For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
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: etetoolkit, Visualization of phylogenetic trees
Teacher
3.5 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
3.5 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
3.6 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
3.6 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: How Can I Plot Go Data Using R Or Any Tools?
Teacher
3.7 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
Teacher
4.0 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
4.0 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Centurion
4.0 years ago,
created 100 posts.
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: Parsing Protein Trees to determine orthologs and paralogs
Good Answer
4.3 years ago,
created an answer that was upvoted at least 5 times.
For A: Parsing A Tree File
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1725 users visited in the last hour