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naturalis / bio-cipres

Phylogenomic analysis on the CIPRES REST portal
MIT License
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Tree construction with IQTree #4

Closed rvosa closed 4 years ago

rvosa commented 4 years ago

IQTree is more or less the standard for building trees from viral genomes. A somewhat costly step that it does by default is to do full model testing to decide on the right model. Perhaps as per Rambaut et al. we might just settle on HKY85+G.

For the clade assignments, bootstrap support would be good (e.g. 1000 replicates), so experiment with how costly that is (-bnni parameter, I think).

rvosa commented 4 years ago 
cipresrun \
    -t IQTREE_XSEDE \
    -p vparam.specify_runtype_=2 \
    -p vparam.specify_dnamodel_=HKY \
    -p vparam.bootstrap_type_=bb \
    -p vparam.use_bnni_=1 \
    -p vparam.num_bootreps_=1000 \
    -p vparam.specify_numparts_=1 \
    -i concatenated.fasta.961.fasta.aln \
    -o output.contree