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 ...
Anthony Guterres's user avatar
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1 answer

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 : ...
pratiksha's user avatar
1 vote
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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 ...
user5520049's user avatar
4 votes
1 answer

Extracting a cytochrome B sequence from NCBI's nucleotide database

Can someone tell the way to extract the fasta sequences for the gene cytb of Acetes japonicus (shrimp important to China and South Korea)? Can I extract them directly from NCBI nucleotide database (i....
Sofia's user avatar
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5 votes
7 answers

calculating nucleotide frequency per column

I have some sequences shown below ...
user3138373's user avatar
11 votes
1 answer

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 ...
Iakov Davydov's user avatar
13 votes
3 answers

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....
Iakov Davydov's user avatar