User: confusedious

gravatar for confusedious
confusedious350
Reputation:
350
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Location:
Australia
Last seen:
2 months, 1 week ago
Joined:
3 years, 8 months ago
Email:
c***********@gmail.com

PhD student working on human population genetics, with a particular interest in recent human evolution and hominid phylogenetics.

R fiddler and Python novice.

More of an anthropologist than a geneticist; I am learning the ropes.

Posts by confusedious

<prev • 93 results • page 1 of 10 • next >
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Answer: A: Multiple alignment and phylogenetic tree resources
... Starting with some nice, easy to use software is good too. If you are on a limited budget, then MEGA offers some nice ways to explore your data. I had the pleasure of attending a talk by the developers of MEGA at the SMBE conference earlier this year - despite it's ease of use, the developers reall ...
written 12 weeks ago by confusedious350
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... A very general one: Using packages without trying to understand what they actually do. A more specific one: Assume that the human mitochondrial reference sequence is the ancestral sequence. ...
written 12 weeks ago by confusedious350
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Comment: C: Software for analysing mitochondrial variants, e.g. synonymous, non-synonymous
... There are thousands of publicly available human mitochondrial sequences on GenBank. ...
written 12 weeks ago by confusedious350
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Comment: C: Software for analysing mitochondrial variants, e.g. synonymous, non-synonymous
... Thank you again for your reply. There is just the one fasta file which is an alignment of human mitochondrial sequences aligned to the rCRS numbering, but I can always generate another fasta file which is just the rCRS if the software needs it. I will look at mummer and see how I go. ...
written 12 weeks ago by confusedious350
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Comment: C: Software for analysing mitochondrial variants, e.g. synonymous, non-synonymous
... Correct. But not between multiple fasta files - I have a fasta file that is an alignment of human mitochondrial sequences. This alignment has been aligned to the rCRS so that the site numbering matches the conventions of human mitochondrial work. From there I want the variable positions to be labe ...
written 12 weeks ago by confusedious350
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Software for analysing mitochondrial variants, e.g. synonymous, non-synonymous
... Hello everyone, I have a large collection of human mitochondrial sequences and would like to characterise variable sites by whether they are coding or non-coding, if coding which codon position they are (i.e. 1st, 2nd or 3rd), and whether the variants present are synonymous or non-synonymous mutati ...
mitochondria written 12 weeks ago by confusedious350
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Comment: C: Measuring the difference or similarity between two phylogenies
... This looks promising - I'll give it a try. Thank you. ...
written 7 months ago by confusedious350
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Comment: C: Measuring the difference or similarity between two phylogenies
... This is very useful - thank you very much. I'll look into these and let you know how I go. ...
written 7 months ago by confusedious350
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Comment: C: Measuring the difference or similarity between two phylogenies
... Thank you for the suggestion - the difficulty that arises with this method for me is that I'm comparing a tree that was made from a complete nucleotide alignment to a tree that was made using a subset of informative positions in the alignment. As such, the distance between the taxa is modified. The ...
written 7 months ago by confusedious350
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Measuring the difference or similarity between two phylogenies
... Hello everyone, I'd like to take two phylogenies for a given nucleotide alignment and create a measure of the similarity between the two alignments. Branch length is not of interest to me in this case, I only care about the branching order or edges shared. I would like to do this in R, and ideally ...
R phylogenetics written 7 months ago by confusedious350 • updated 7 months ago by jhc2.4k

Latest awards to confusedious

Great Question 7 months ago, created a question with more than 5,000 views. For Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Wright'S Fst And Weir & Cockerham'S Fst Estimator - Simple Explanation Of The Difference
Popular Question 8 months ago, created a question with more than 1,000 views. For Mapping Fst Values To A Manhattan Plot By Rs#
Epic Question 12 months ago, created a question with more than 10,000 views. For Wright'S Fst And Weir & Cockerham'S Fst Estimator - Simple Explanation Of The Difference
Popular Question 13 months ago, created a question with more than 1,000 views. For Mapping Fst Values To A Manhattan Plot By Rs#
Scholar 13 months ago, created an answer that has been accepted. For A: PAUP: Multiple individuals as one branch
Popular Question 21 months ago, created a question with more than 1,000 views. For Collapsing poorly supported nodes into polytomies in R - using 'Phangorn' and 'ape'
Popular Question 21 months ago, created a question with more than 1,000 views. For Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Quick And Easy Way To Map Snps To Genes (Or Regions Near Genes)
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists
Supporter 2.9 years ago, voted at least 25 times.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: How Does Average Heterozygosity Relate To Alellic Frequency Data
Student 2.9 years ago, asked a question with at least 3 up-votes. For Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists
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