User: mimi

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mimi20
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Posts by mimi

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Comment: C: Haplotypic diversity with pegas package error
... Yes, I used it, but there is no fault. I would like to calculate the haplotypic diversity of 100 aligned bacterial genomes. (fasta file) ...
written 13 months ago by mimi20
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Haplotypic diversity with pegas package error
... Hello, I'm trying to use haploNet function of {pegas} to plot a haplotype network, but i`m having an error. I can't build a haplotype net with the following script: library(pegas) S<- read.dna(file = "C:/Users/.....file.fasta", format ="fasta") h<-haplotype(S) net<-haploNe ...
phylogeny R genomic haplotypic diversity written 13 months ago by mimi20 • updated 13 months ago by zx87547.3k
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Comment: C: how to use the pegas package to calculate tajima D
... My files are genome sequences after doing an alignment. My problem is that I divided my 100 genomes into 6 populations, and I would like to calculate the Dtajima for 6. Unfortunately I have this fault that I can not understand. enter link description here Thank you setwd("C:/Users/....") ...
written 13 months ago by mimi20
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Comment: C: how to use the pegas package to calculate tajima D
... https://www.biostars.org/p/307819/#307825 ...
written 13 months ago by mimi20
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Comment: C: how to calculate the haplotypic, nucleotidic diversity and theta of watterson
... Hello and thank you for your answer. The article itself does not answer my questions, I used the pdf manual (much more detailed and clear).[enter link description here][1] My files are genome sequences after doing an alignment. My problem is that I divided my 100 genomes into 6 populations, and I ...
written 13 months ago by mimi20
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Comment: C: how to use the pegas package to calculate tajima D
... Myexample<- read.FASTA(file="alignment_100.fasta_SNP.fasta") ...
written 13 months ago by mimi20
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Comment: C: converter format asn to gff
... Oups! Sorry @genomax ...
written 23 months ago by mimi20
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Comment: A: converter format asn to gff
... Sorry ! Can I convert this xml format to gff3 ? Thanks ...
written 23 months ago by mimi20
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Comment: A: converter format asn to gff
... The asn format to prosplign : Seq-align ::= { type disc, dim 2, score { { id str "num_ident", value int 0 }, { id str "num_positives", value int 0 }, { id str "num_negatives", v ...
written 23 months ago by mimi20 • updated 23 months ago by genomax67k
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converter format asn to gff
... Hi, I used prosplign ( https://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html). It generated a file ASN, but I need a gff3 format Do you know an affective converter? I used `asn2flat -i file.asn -format gff3 -o out` (but it does not support the gff3 format, it advises to use annotw ...
asn gff3 written 23 months ago by mimi20

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