User: a1ultima

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a1ultima750
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750
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London
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https://www.linkedin.c...
Last seen:
2 days, 4 hours ago
Joined:
6 years, 7 months ago
Email:
a****@ic.ac.uk

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Posts by a1ultima

<prev • 70 results • page 1 of 7 • next >
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Comment: C: Best Practices/Softwares To Calculate Ka/Ks Ratio
... Hi Assalm, I've only ever got it to work with pairs ...
written 2.6 years ago by a1ultima750
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Comment: C: Ka/Ks Ratio For Within A Gene - Very Confused !!
... Have a look at the bottom of the best answer on this biostars Q: https://www.biostars.org/p/5817/#234442 ...
written 3.3 years ago by a1ultima750
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Comment: C: What is GFF3 and how to extract genomic sequences from it?
... Seems the gffread link is now broken, just a head's up ...
written 3.4 years ago by a1ultima750
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Answer: A: How To Calculate The Number Of Potential Synonymous And Nonsynonynous Sites
... How about [this][1]? But if you would prefer to see code (instead of math), then have a look at [changes.py][3] (Python code). But perhaps my documentation was not clear, so just ask me for clarification. Or have a look at some of the links mentioned in a [related Biostars post][4]. If none of t ...
written 3.4 years ago by a1ultima750
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Comment: C: Best Practices/Softwares To Calculate Ka/Ks Ratio
... For all who have asked for the dN/dS Python file, it is finally on GitHub, I really do apologize for how long I have taken to get back to some of you. This Python file I am sharing is part of a bigger pipeline, but I hope I have documented it well enough now so that you can just take this part and p ...
written 3.4 years ago by a1ultima750
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Comment: C: Best Practices/Softwares To Calculate Ka/Ks Ratio
... I am really sorry about the embarassingly long wait before giving the R script for calculating error-bars for your dN/dS analyses. For anybody who still needs it, I've put the script on GitHub with instructions on what you need to do to get it to work in the README.md: [https://github.com/a1ultim ...
written 3.6 years ago by a1ultima750
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Which ligands bind (are sensed by) these Odorant Binding Proteins?
... I have a list of odorant binding protein (OBP) IDs, from the malarial mosquito Anopheles gambiae, and I would like to know which ligands they bind to.  I would greatly appreciate tips or links to resources to help me identify which ligands these proteins bind to.  Here are the list of protein IDs: ...
protein odorant ligand written 4.6 years ago by a1ultima750
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Estimate gene flow between two populations?
... Imagine there are two populations X and Y, and for each population you have the genotypes of each individual in that population (e.g. Aa, AA, aa, etc.), but for multiple loci (e.g. AABb). How could one calculate the gene flow between population X and population Y? An answer would ideally recommend ...
population-genetics genetics fst gene-flow written 4.9 years ago by a1ultima750
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Comment: C: Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
... Yep here (sorry for the late reply): https://github.com/biopython/biopython/issues/483 ...
written 5.3 years ago by a1ultima750
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Comment: C: How Well Is A Masters/Phd In Computational Biology Accepted In The Computer Scie
... Perhaps Stack: Academia and/or Research Gate ...
written 5.4 years ago by a1ultima750

Latest awards to a1ultima

Great Question 4 months ago, created a question with more than 5,000 views. For Shannon entropy of a DNA motif?
Great Question 20 months ago, created a question with more than 5,000 views. For Shannon entropy of a DNA motif?
Popular Question 20 months ago, created a question with more than 1,000 views. For Which cut-off for collapsing this tree?
Popular Question 22 months ago, created a question with more than 1,000 views. For Which cut-off for collapsing this tree?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Which cut-off for collapsing this tree?
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Shannon entropy of a DNA motif?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How Easy Is It To Carry Out De Novo Sequence Assembly?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Alignio Gives 'Assertionerror' When Reading Emboss Alignment Files
Student 3.3 years ago, asked a question with at least 3 up-votes. For Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Predicting Host-Pathogen Gene Interaction Networks
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Predicting Host-Pathogen Gene Interaction Networks
Good Answer 4.2 years ago, created an answer that was upvoted at least 5 times. For A: Homologous Sequence Identity
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Predicting Host-Pathogen Gene Interaction Networks
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Shannon entropy of a DNA motif?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How Easy Is It To Carry Out De Novo Sequence Assembly?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Collapse Clades In A Newick Tree With Average Distance To Tips < X
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Collapse Clades In A Newick Tree With Average Distance To Tips < X
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: Homologous Sequence Identity
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Alignio Gives 'Assertionerror' When Reading Emboss Alignment Files
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Codon Alignment Via Python?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Shannon entropy of a DNA motif?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Collapse Clades In A Newick Tree With Average Distance To Tips < X
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Sliding Window Ka/Ks (Dn/Ds) Analysis Via Python?

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