User: vicky

gravatar for vicky
vicky20
Reputation:
20
Status:
New User
Location:
Germany
Last seen:
3 weeks, 3 days ago
Joined:
7 years, 1 month ago
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v*************@gmail.com

Posts by vicky

<prev • 21 results • page 1 of 3 • next >
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Extraction of subset of population from Ancestrymap files (.geno, .ind., .snp)
... Hi I have got the ancestry map files (.geno, .ind, .snp) files with 1000 individuals from 200 populations. I want to extract a subset (20) of populations from these files. Is there any program to do this. I want run later SmartPca over these files. thanks ...
plink smartpca written 28 days ago by vicky20
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Plotting common SNPs from four individual from a vcf file
... Hi I have got the vcf file with the SNP informations from four individuals. I want to make a Venn diagram (or another graphical display of the SNPs) of the SNPs? To see how many SNPs are shared and private between these four individuals. Is there a tool who does it. My data looks like this : # ...
snp written 8 months ago by vicky20 • updated 8 months ago by dariober9.5k
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PSMC plot (Effective population size)
... Hi PSMC output a .psmc file but is there a method to calculate the mean effective population size. Where exactly is this information in the file.   Best ...
next-gen written 2.9 years ago by vicky20
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Principal component analyses
... Hi All If some one who has done Principal component analysis (PCA) can tell me what is the minimum number of genomes you need for this analysis. I want to run this analysis on some mammalian genome and was wondering what can be the minimum number, some one told me its around four individual genomes ...
genome written 3.1 years ago by vicky20 • updated 3.1 years ago by Vincent Laufer1000
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Submission of mitochondrial sequence to ENA
... Hi All I have got mitochondrial sequences in fasta format which I need to submit in ENA. I need to functionally annotated it and submit in INSDC feature table format http://www.insdc.org/files/feature_table.html. If some one can has submitted the sequences earlier and help me how to convert the f ...
ena written 3.3 years ago by vicky20 • updated 3.2 years ago by c67amid0
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Calculating Heterozygosity of the genome
... Hi All   I have a genome data with heterozygous sites marked as (M,R,W,S,Y,R,S,K,W,Y,K). Can I some how calculate the average heterozygosity of the genome.       ...
heterozygosity written 3.4 years ago by vicky20
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Comment: C: Phylogentic tree construction using only the synonymous sites
... Thanks of the reply. In the sea-view http://pbil.univ-lyon1.fr/software/seaview3.html , I found that in NJ  method you can consider the Ks sites to construct the tree. Regarding why I want to use that, one of the reviewers of my paper asked for it. He believes that divergence time gets affected if I ...
written 3.6 years ago by vicky20
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Phylogentic tree construction using only the synonymous sites
... Hi   Do any one knows any program other than Mega (Phylogenetic package) which can make phylogenetic tree only considering synonymous sites? Thanks ...
phylogeny written 3.6 years ago by vicky20 • updated 3.6 years ago by Josh Herr5.6k
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Comment: C: ABBA and BAAB test of admixture (D test)
... Thanks for reply. I just used the example here for humans I have different species. I just had the doubt that the outgroup species in the software mentioned above cannot be used inside the three species say (A,B:C) which says it should be like this (A,B:C,O). Now the outgroup will be ancestral stat ...
written 3.7 years ago by vicky20
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Convert repeat masked out file to bed file format
... Hi Can any one tell me a program or script which I can use to convert the repeat masked.out file to .bed file.   Thanks   ...
next-gen written 3.7 years ago by vicky20 • updated 3.7 years ago by Devon Ryan85k

Latest awards to vicky

Popular Question 6 months ago, created a question with more than 1,000 views. For PSMC plot (Effective population size)
Popular Question 6 months ago, created a question with more than 1,000 views. For Principal component analyses
Popular Question 22 months ago, created a question with more than 1,000 views. For Principal component analyses
Popular Question 22 months ago, created a question with more than 1,000 views. For Softwares To Make Saturation Plot For Codon Postion
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Softwares To Make Saturation Plot For Codon Postion
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Likelihood Ratio Test Using The Codeml
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Principal component analyses
Popular Question 2.9 years ago, created a question with more than 1,000 views. For ABBA and BAAB test of admixture (D test)
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GATK vcf file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Likelihood Ratio Test Using The Codeml

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