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zackbatist / open-archaeo

A list of open source archaeological software and resources
https://open-archaeo.info
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New tag: aDNA kinship #25

Open nevrome opened 3 years ago

nevrome commented 3 years ago

I suggest to add a new tag aDNA kinship. This is a topic with obvious relevance for archaeology. Papers about biological kinship are usually developed in close collaboration of geneticists and archaeologists.

The following software tools could be added to this tag:

@jfy133 Do you know other software tools that fall into this category? Maybe you, @MaiteRivollat? I know you worked extensively on this topic and probably dived deeply into the available software tools.

jfy133 commented 3 years ago

You got the ones I already knew.

I guess could consider: https://github.com/ANGSD/NgsRelate

as "from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes" - not specfically aDNA but I suspect is related

zackbatist commented 3 years ago

New tag and new items added. Feel free to suggest any additional updates or new entries here.

MaiteRivollat commented 3 years ago

Hi all, sorry for the delay of my reaction.

I know about a few more methods, but haven't used them myself... Here is a list with relevant webpages:

IBSrelate (coverage >=2x): https://onlinelibrary.wiley.com/doi/full/10.1111/mec.14954 http://www.popgen.dk/software/index.php/IBSrelate

SEEKIN: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007021 https://github.com/chaolongwang/SEEKIN/

Hope it can help!

Le ven. 23 juil. 2021 à 13:13, Zack Batist @.***> a écrit :

New tag and new items added. Feel free to suggest any additional updates or new entries here.

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