User: jhc
jhc • 2.8k
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- Joined:
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Posts by jhc
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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 13 months ago by
jhc • 2.8k
0
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1
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943
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... you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/ ...
written 2.1 years ago by
jhc • 2.8k
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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 2.3 years ago by
jhc • 2.8k
2
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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 2.3 years ago by
jhc • 2.8k
1
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496
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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 2.3 years ago by
jhc • 2.8k
5
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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 2.5 years ago by
jhc • 2.8k
0
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2
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1.2k
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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 2.6 years ago by
jhc • 2.8k
1
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0
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1.1k
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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 2.6 years ago by
jhc • 2.8k
0
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2
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1.9k
views
2
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... just the NOG, COGs, arCOGs and KOGs are stable ...
written 3.1 years ago by
jhc • 2.8k
0
votes
1
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1.2k
views
1
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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 3.2 years ago by
jhc • 2.8k
Latest awards to jhc
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10 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
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For When Is Dna Better Choice Than Aminoacids For Multiple Sequence Alignments And Phylogenetic Reconstruction?
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For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
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For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
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For A: etetoolkit, Visualization of phylogenetic trees
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For ETE build: from sequences to phylogenetic trees with just a single command line.
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For A: etetoolkit, Visualization of phylogenetic trees
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For A: Parsing Protein Trees to determine orthologs and paralogs
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For A: Can I Choose An Outgroup Based On Phylogenetic Tree Structure Alone?
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For A: Parsing Protein Trees to determine orthologs and paralogs
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For A: etetoolkit, Visualization of phylogenetic trees
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For A: How Can I Plot Go Data Using R Or Any Tools?
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For ETE build: from sequences to phylogenetic trees with just a single command line.
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For A: How Can I Plot Go Data Using R Or Any Tools?
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For A: Parsing Protein Trees to determine orthologs and paralogs
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For A: How Can I Plot Go Data Using R Or Any Tools?
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For A: Program for searching for a specific partition within a set of phylogenetic tree
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For A: How Can I Plot Go Data Using R Or Any Tools?
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For A: Parsing Protein Trees to determine orthologs and paralogs
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For A: Parsing Protein Trees to determine orthologs and paralogs
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For A: Parsing A Tree File
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