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We want to run NetRAX on this empirical dataset (from https://advances.sciencemag.org/content/5/5/eaav9188) which is available for download at https://bioweb.supagro.inra.fr/WheatRelativeHistory/index.php?menu=download
- We need the IndividualAlignments data, which we merge together into one big MSA (I wrote a script for it here: https://github.com/lutteropp/NetRAX/blob/master/scripts/merge_gene_alignments.py)
- Each gene is its own partition.
- The standard RAxML model (GTR+GAMMA) is okay
- We have 47 individuals over 17 species in the dataset.
- There are 1387815 patterns in the merged MSA, and 8738 partitions
- In order to create a MSA based on species, we can either use extended DNA alphabet or, more elegant version: Chapter 5 of Alexeys PhD thesis (https://cme.h-its.org/exelixis/pubs/dissAlexey.pdf)
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