User: natasha

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natasha100
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Posts by natasha

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formating for fineSTRUCTURE input
... Hi I would like to use fineSTRUCTURE to access the population structure of a bacterial species. Thus I will be inputting SNP data. However, I don't understand how to create the 'phased' data format that fineSTRUCTURE requires. The fineSTRUCTURE manual lists multiple programmes to help with this ph ...
format input finestructure written 2.5 years ago by natasha100
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Comparing branch lengths of phylogenies
... I have generated 2 phylogenies for same sequence data, however for one of these phylogenies I have removed recombination. The topology of the trees are therefore the same but the branch lengths are now different. Is there a way to quantify this - as in, is there an algorithm I can use to show a stat ...
phylogeny branch length recombination written 2.7 years ago by natasha100 • updated 2.7 years ago by dago2.5k
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Genes involved in recombination
... Sorry if this is a bit of a silly question, but I'm looking for a few opinions on my methods.... I have a core genome alignment of 50 isolates, from which I have detected multiple regions of recombination (either in a single isolate or in multiple). I would like to analyse the genes that are affec ...
annotation genes recombination written 2.8 years ago by natasha100
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Calculate SNPs per branch on RAxML tree
... Hi How can I calculate the number of SNPs per branch on my ML tree generated in RAxML? I know how to create a matrix of branch lengths, but I just want SNPs. Am I missing something really easy??! ...
phylogeny raxml snp written 2.8 years ago by natasha100
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Comment: C: Software for plotting gene presence absence matrix
... 50 strains. I make a mistake, I have 1800 genes to plot not 4000. ...
written 2.8 years ago by natasha100
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Comment: C: Software for plotting gene presence absence matrix
... Because I am looking at bacteria of the the same ST, the accessory genes are what make each isolate unique from one another. Sorry I made a mistake -- I only have 1800 genes to plot (4000 is the core genome) ...
written 2.8 years ago by natasha100
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Software for plotting gene presence absence matrix
... Hi I have a gene presence-absence matrix of accessory genes, for multiple strains of bacteria. I would like to produce a good figure with this data, and maybe include a tree as well . I was wondering what the best software programmes are available to do this? As I have >4000 genes, I don't each ...
R accessory genes python matrix written 2.8 years ago by natasha100 • updated 2.8 years ago by Philipp Bayer6.0k
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Codeml error - format problem?
... Hi I am having problems trying to get codeml to run. I have read through all the other posts for similar issues on biostars and tried everything I can think of. I am inputting a tree (newick format) and a gene alignment of the coding regions for 57 bacterial isolates (phylip format), as well as a . ...
dn/ds paml codeml written 2.8 years ago by natasha100 • updated 2.8 years ago by rstuder0
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Comment: C: Create a presence absence matrix in R for gene data
... Thank you, this worked perfectly ...
written 2.8 years ago by natasha100
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Create a presence absence matrix in R for gene data
... Hi I am new to R and would like to create a presence absence matrix for my gene data. My data at the moment looks like this; Isolate 1 2 3 4 Gene1 N/A Vp_2003 Vp_2003 Vp_2004 Gene2 Vp_4590 N/A N/A N/A Gene3 Vp_3333 Vp_3333 Vp ...
R written 2.8 years ago by natasha100 • updated 2.8 years ago by Michael Dondrup46k

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