Questions tagged [mtdna]

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

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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
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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
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-1 votes
1 answer
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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
189 views

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