User: fransua

gravatar for fransua
fransua390
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390
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Spain
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2 months, 1 week ago
Joined:
6 years, 9 months ago
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Posts by fransua

<prev • 23 results • page 1 of 3 • next >
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Comment: C: How to create chain file to change genome coordinates from one genome version to
... I just found this: https://github.com/wurmlab/flo haven't tried yet, but it seems to do the job... ...
written 18 months ago by fransua390
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Answer: A: Matplotlib comprehensive chromosome drawing
... Fantastic work. I noticed a little mistake in the chromosome_collection function. line 61, facecolors should be group['colors'] and not df['colors']. thanks a lot anyway @Ryan_Dale ...
written 2.1 years ago by fransua390
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geneid.txt and knownGene.txt files in UCSC database to retrieve exon position in non-human species
... Hi, I would like to get the exon position of several non-human species, for this the best option would be to use the knownGene.txt file as mentioned by Pierre Lindenbaum. The problem is that this file is available for human and mouse but not for other species. The other file that is present in non ...
database ucsc written 2.3 years ago by fransua390 • updated 2.3 years ago by stevenlang123130
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Answer: A: Which software can be used to visualize phylogenetic trees with a large number o
... Maybe ETE solves your problem, I know the developper has been focussing lately on being able to visualize very large trees. It's a Python library, however it is quite straight forward if you only want to display and save a tree. ...
written 3.8 years ago by fransua390
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Comment: C: How To Draw A Rooted Phylogenetic Tree
... programatically? ...
written 4.7 years ago by fransua390
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Answer: A: How To Best Calculate Dn/Ds Ratios Of Viral Genomes
... Recently ETE2 program (http://ete.cgenomics.org) has come with a new version that completely wraps CodeML and allows to represent visually the results. From my experience CodeML might be easier to use in this way (you can check the tutorial relative to this new part: http://pythonhosted.org/ete2/tut ...
written 4.7 years ago by fransua390
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Answer: A: Mouse Protein Homologs Of 380 Drosophila Genes
... it is not exactly what you asked for, but you may be able to build most of your query through biomart: http://www.ensembl.org/biomart/martview/ef14953c93b865c9693d3637ee65cd3d just paste the IDs of your 380 Drosophila genes in the filter tab. ...
written 5.3 years ago by fransua390
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Comment: C: Running Codeml On Unrooted Tree
... At this point I have a doubt... Usually I use rooted trees with "clock=0", because I believe that it does not matter if you are not intersted in the estimations relative to the outgroup sequence (exact position of the root)... but I am not sure actually if this changes. Do you have an idea? ...
written 5.5 years ago by fransua390
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Comment: C: Estimating Purifying Selection With Codeml (Paml)
... you should use model paasing LRT, however as there is no BEB under M1 model, and your are not loknig for sites under positive selection, it might not be too bad to use M2a BEB results, for a descriptive analysis of the strngth of selection along the sequence. the methodology you propose may not allo ...
written 5.6 years ago by fransua390
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Comment: C: Estimating Purifying Selection With Codeml (Paml)
... M1a model assumes 2 classes of sites, the first with omega<1 and the second with omega=1. (I edit to complete the answer) ...
written 5.6 years ago by fransua390

Latest awards to fransua

Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Counting Repeat Sequence
Appreciated 24 months ago, created a post with more than 5 votes. For A: Counting Repeat Sequence
Appreciated 24 months ago, created a post with more than 5 votes. For A: How To Best Calculate Dn/Ds Ratios Of Viral Genomes
Voter 2.1 years ago, voted more than 100 times.
Supporter 4.2 years ago, voted at least 25 times.
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: How To Best Calculate Dn/Ds Ratios Of Viral Genomes
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Estimating Purifying Selection With Codeml (Paml)
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Where Can I Download Nucleotide Sequences Of Bacterial Genes?
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: When Is Dna Better Choice Than Aminoacids For Multiple Sequence Alignments And P
Good Answer 6.7 years ago, created an answer that was upvoted at least 5 times. For A: Counting Repeat Sequence
Teacher 6.7 years ago, created an answer with at least 3 up-votes. For A: Counting Repeat Sequence
Appreciated 6.7 years ago, created a post with more than 5 votes. For A: Counting Repeat Sequence

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