make_starting_tree: Generate a starting tree for beast
In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses
Description
Usage
Arguments
Value
Description
This assumes the sequence data are in the format generated by prep_tip_labels_phydyn
Requirements:
1) Fasta must have labels matching this form hCoV-19/Netherlands/Haarlem_1363688/2020|EPI_ISL_413572|2020-03-01|2020.16393442623|_Il
2) iqtree must be installed and in the environment
Usage
1
make_starting_tree(fn, treeofn = "startTree.nwk", ncpu = 4)
Arguments
fn
File name of input alignment. Must be in current working directory
treeofn
File name for output tree (newick)
ncpu
Integer number of cores
Value
Will write the starting tree and returns the treedater tree
emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.
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Description Usage Arguments Value
Description
This assumes the sequence data are in the format generated by prep_tip_labels_phydyn Requirements: 1) Fasta must have labels matching this form hCoV-19/Netherlands/Haarlem_1363688/2020|EPI_ISL_413572|2020-03-01|2020.16393442623|_Il 2) iqtree must be installed and in the environment
Usage
1 | make_starting_tree(fn, treeofn = "startTree.nwk", ncpu = 4)
|
Arguments
fn |
File name of input alignment. Must be in current working directory |
treeofn |
File name for output tree (newick) |
ncpu |
Integer number of cores |
Value
Will write the starting tree and returns the treedater tree
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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