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Results tagged with phylogenetics
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user 9311
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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What are the symbols of $*$ and '$\_$' in an unknown alignment format for HLA data from the ...
Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of ea …
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Minimal working example for phylogenetic tree construction in R using an alignment of DNA st...
I am looking at how to build a phylogenetic tree in R from aligned genetic information (dna sequences). There are multiple tutorials on how to go about this task eg tutorial1, tutorial2 ("ape" docs), …
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Minimal working example for phylogenetic tree construction in R using an alignment of DNA st...
A key difference from many examples provided is that they assume that the data provided is in the form of sequences rather than an already aligned sequence alignment.
library("Biostrings")
library("se …
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How to create Phylogenetic Trees from fasta files in Python or R?
(if I understand your situation correctly) https://www.rdocumentation.org/packages/seqinr/versions/3.6-1/topics/read.alignment shows how to use the function read.alignment which can take fasta msf etc …
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Accepted
Motivation behind the neighbor-joining distance matrix recomputation
Let's look at the components of the equation one by one first since it is easier to describe each part on its own. We can do this because they are added together in computing $Q_{ij}$. Component1, $(m …
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