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Questions tagged [mtdna]

Mitochondrial DNA. Questions specific to mitochondrial DNA, such as annotation, inheritance, heteroplasmy.

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Problem while mapping reads to mtDNA (SortSam)

I am trying to map MiSeq reads to a reference genome and extract mutations using MToolBox, which implements gsnap, GATK, Picard, and other tools. When running the tool with example data, there were no ...
uri's user avatar
  • 85
1 vote
1 answer

Compare FASTQ reconstructions to mtDNA

I have some doubts in how to proceed to compare ancient mtDNA with modern mtDNA. A little more context: The problem: I have some FASTQs associated with a given FASTA. They contain mtDNA. My goal is to ...
dyxcvi's user avatar
  • 37
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Why is mtDNA not labelled as such for many organisms?

Also posted on biostars While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure ...
George X.'s user avatar
1 vote
1 answer

How to remove third codon positions from a charset in iqtree?

I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets: ...
Francesco De Giglio's user avatar
4 votes
1 answer

How does one distinguish nuclear DNA from mitochondrial DNA when doing WGS?

I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene ...
Caterina's user avatar
  • 307
-1 votes
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Unable to Install PGDSpider using Ubuntu and wine

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
Mollie Passacantando's user avatar
1 vote
1 answer

Heteroplasmy Calculation

For calculating heteroplasmy in mtDNA I was using MitoSeek, the tool provides position wise heteroplasmy percentage. So, will it be wise to add up all sites to get a position-wise percentage in a ...
arup's user avatar
  • 604