User: confusedious

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confusedious370
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Australia
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1 month, 1 week ago
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4 years ago
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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 • 95 results • page 1 of 10 • next >
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Answer: A: Software for counting mutations over a tree
... I found that an estimation of the maximum mutation count at each position can be obtained using Fluxus Network's statistics tool after building a Median Joining network. See: http://www.fluxus-engineering.com/sharenet.htm ...
written 11 weeks ago by confusedious370
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Comment: C: Software for counting mutations over a tree
... Thank you for the suggestions. I have tried with these packages, but have only been able to get a mutation count for the whole alignment/tree combination, not a count for individual informative sites. ...
written 11 weeks ago by confusedious370
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Answer: A: Looking For An Easy To Use Tool To Analyse A Gene Set For Enrichment Of Immunolo
... I ended up using GOrilla which worked quite well. Worth a look. ...
written 3 months ago by confusedious370
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Software for counting mutations over a tree
... Hi everyone, I have a nucleotide alignment in .fasta format and a phylogenetic tree for these data in .newick format. I'd like to find some software that can count how many times each variable position in the alignment needs to change over a given tree tree (interpreting the mutations in the most ...
phylogenetics written 3 months ago by confusedious370 • updated 11 weeks ago by jhc2.5k
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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 7 months ago by confusedious370
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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 7 months ago by confusedious370
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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 7 months ago by confusedious370
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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 7 months ago by confusedious370
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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 7 months ago by confusedious370
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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 7 months ago by confusedious370

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Remove rows in a matrix containing Hamming distance less than a set value
Scholar 11 weeks ago, created an answer that has been accepted. For A: PAUP: Multiple individuals as one branch
Scholar 3 months ago, created an answer that has been accepted. For A: PAUP: Multiple individuals as one branch
Popular Question 6 months ago, created a question with more than 1,000 views. For Get Snps For A List Of Gene Symbols In A Text File As A Single Column
Popular Question 6 months ago, created a question with more than 1,000 views. For Quick And Easy Way To Map Snps To Genes (Or Regions Near Genes)
Great Question 11 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 11 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 12 months ago, created a question with more than 1,000 views. For Mapping Fst Values To A Manhattan Plot By Rs#
Epic Question 16 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 18 months ago, created a question with more than 1,000 views. For Mapping Fst Values To A Manhattan Plot By Rs#
Scholar 18 months ago, created an answer that has been accepted. For A: PAUP: Multiple individuals as one branch
Popular Question 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists
Popular Question 3.3 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)
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