TaxOnTree Files

TaxOnTree - Including taxonomic information on your phylogenetic tree


This folder contains all necessary files to run TaxOnTree offline:

	* BLAST databases used in our web tool (biodados.icb.ufmg.br/taxontree).
	* TaxOnTree MySQL database
	
	Obs.: Besides these files, you will also need to install StandAlone BLAST+
	in your machine to run TaxOnTree offline. 
	
(a)	BLAST databases
	
	To use it in a local machine just download one of them and extract it by 
	the command:

	> tar -zxvf database_name.tgz

	For splitted database,  download  all  parts first and then extract the 
	content by the command:

	> cat splitted_database.tgz-part* | tar -zxv

	To use it with the command line version of TaxOnTree just  add  to  the 
	TaxOnTree  command  line  the  parameter -db <database_name>.  If  your 
	database is not in the same location, just  inform  the  path  to  your 
	database.

	Example:
	> ./taxontree -singleQueryID 4757876 -db path/to/database/database_name


	Description of each database in this folder:

	i) uniprot_proteome_db.tgz

		This database contains sequences from UniprotKB reference proteomes.
		Sequences from this database was downloaded in Oct 11, 2015.
		
		More information about UniprotKB Reference Proteomes at:
		http://www.uniprot.org/help/reference_proteome
		
	ii) refseq.protein.72.tgz-part*

		This database contains sequences from RefSeq version 72 of NCBI.
		Sequences from this database was downloaded in Oct 7, 2015.
		
		To  use  the  full  RefSeq  database, use  "refseq.protein"  as 
		database_name.
		
		If you want to filter your BLAST search only  whithin  proteins 
		with complete status (not  fragmented  protein),  database_name
		should be "refseq.protein.complete".
		
		More information about RefSeq version 72 at:
		ftp://ftp.ncbi.nlm.nih.gov/refseq/release/README
		
(b) MySQL database (taxontree.sql.tgz)

	MySQL Dump file containing all information about gene and taxonomy ID for 
	each protein accession. Download it and then extract it by the command:
	
	> tar -zxvf taxontree.sql.tgz
	
	Then, upload the extracted file to your MySQL account by the commad:
	
	> mysql -u <username> -p < taxontree.sql
	
	or in the MySQL environment:
	
	mysql> source taxontree.sql
	
	To configure TaxOnTree to use the local MySQL database, set the MySQL account user name 
	and password in CONFIG.xml file (See CONFIG.xml). Then, in the TaxOnTree command
	line, add the paramenter -mysql. Example:
	
	> ./taxontree -querysingleid 123456789 -db <database_name> -mysql