export_accnet_aln: Export accesory genome binary multi-alignment.
In irycisBioinfo/PATO: Pangenome Analysis Toolkit
View source: R/export_accnet_aln.R
export_accnet_aln R Documentation
Export accesory genome binary multi-alignment.
Description
This function write the presence/abscence matrix into a binary alignment file
that can be use with RaxML or iqtree to build a phylogenetic tree.
Usage
export_accnet_aln(accnet, file, min_freq = 3)
Arguments
accnet
An accnet object
file
Output filename
min_freq
Minimun frequency of a gene/proteins to include in the alignment
Details
Some phylogenetic tree inference tool allow as input binary aligments. We recommend
to use RAxML-NG or iQtree to inference an accessory genome tree.
irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.
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View source: R/export_accnet_aln.R
| export_accnet_aln | R Documentation |
Export accesory genome binary multi-alignment.
Description
This function write the presence/abscence matrix into a binary alignment file that can be use with RaxML or iqtree to build a phylogenetic tree.
Usage
export_accnet_aln(accnet, file, min_freq = 3)
Arguments
accnet |
An accnet object |
file |
Output filename |
min_freq |
Minimun frequency of a gene/proteins to include in the alignment |
Details
Some phylogenetic tree inference tool allow as input binary aligments. We recommend to use RAxML-NG or iQtree to inference an accessory genome 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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