Questions tagged [nucleotide-models]
An important basis of modern phylogenetics describing the mathematical basis of mutation
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What does instantaneous rate matrix mean?
PhyML is a tool used for maximum likelihood estimation analysis.
I was running a PhyML analysis to check the rate of nucleotide change in DNA sequences and in the PhyML output, there are rate ...
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1answer
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how to generate structure file from blast results of an input sequence
I have tried to incorporate blast in my application using biopython.i could extract the blast results but now i want to extract the structure file corresponding matches. My code is :
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1answer
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How can i get data set of illness and not illness people?
I'm reading a virology paper where the authors made a classification for the patients as to whether they had a specific disease outcome or not against the underlying sequence ...
The research focused ...
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0answers
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Extract sequence from nucleotide databse
Can someone tell the way to extract the fasta sequences of gene Cytb? Can I extract them in the nucleotide database?
For instance, I'm trying to fetch the fasta data of Acetes japonicus of cytb gene. ...
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7answers
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1answer
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State of the art mutation simulation software
There are many features affecting mutation probabilities, e.g. CpG mutations are 10-fold more likely than other types of mutations.
Is there a model (preferably with software) which can take two ...
12
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3answers
150 views
What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?
Let's say I want to construct a phylogenetic tree based on orthologous nucleotide sequences; I do not want to use protein sequences to have a better resolution. These species have different GC-content....
