megatree-ncbi-loader - Loads the NCBI taxonomy dump into a database
megatree-ncbi-loader -nodes <file> -names <file> -d <file> [-vhm]
Location of the nodes.dmp file from the NCBI taxonomy dump, i.e. as contained in the archive located here as of 2017-02-03: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
nodes.dmp
Location of the names.dmp file from the NCBI taxonomy dump, i.e. as contained in the archive located here as of 2017-02-03: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
names.dmp
Location of a database file, compatible with sqlite3, which will be produced. This file can not yet exist. If it does, an error message will be emitted and the program will quit.
Optional.
With this option, more feedback messages are written during processing. This option can be used multiple times, which increases the verbosity further.
Prints help message / documentation.
Prints manual page. Additional information is available in the documentation, i.e. perldoc megatree-ncbi-loader
perldoc megatree-ncbi-loader
This program produces a database file from the NCBI taxonomy dump. Such a database provides much quicker random access to the taxonomy tree then by processing the flat files. The example trees that are referred to by the release of Bio::Phylo::Forest::DBTree have been produced in this way. They can be accessed by an API that is compatible with Bio::Phylo, but much more scalable. An example of such API usage is presented by the megatree-pruner script.
To install Bio::Phylo::Forest::DBTree, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo::Forest::DBTree
CPAN shell
perl -MCPAN -e shell install Bio::Phylo::Forest::DBTree
For more information on module installation, please visit the detailed CPAN module installation guide.