TreeFam
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Tree families database The Sanger Institute Beijing Genomics Institute
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MySQL Dump

TreeFam manages almost all the data in MySQL database. MySQL dump can be downloaded at ftp://ftp.sanger.ac.uk/pub/treefam/release-4.0/MySQL which contains the SQL scripts to create tables and TAB-delimited data files for each table. These tables are relatively independent of each other. The fields of tables are also self-explained, which will facilitate text-based programming.

genes sequence ID, gene name, transcript name, symbol, description and so on
speciestax ID, taxonomy name, abbr. name, and common name of species
map genomic locations of transcripts; in UCSC format
pfam Pfam predictions for each sequence
aa_seq amino acid sequences
nt_seq nucleotide sequences
familyAaccessions, symbols and names of TreeFam-A families
familyBbasic information on TreeFam-B families
famB2A relation between curated TreeFam-A and original TreeFam-B families
phigs PhIGs accessions of TreeFam-B families
trees phylogenetic trees in NHX format
misc_feat symbols and names of B families; curators of A families
misc_key descriptions of `key' used in `misc_feat' table
aa_seed_align amino acids multialignment for TreeFam-A seeds in CIGAR format
aa_full_align full multialignment for both A and B families in CIGAR format
hmmer HMMer scores of matched sequences

Flat Files

TreeFam alignment and trees are also available as flat files, which can be downloaded at ftp://ftp.sanger.ac.uk/pub/treefam/release-4.0/flat_file. File aln-4.0.tar.gz contains amino acids and nucleotide multialignment for all the families . Phylogenetic trees are available as trees-4.0.tgz.


Subversion Access

Source codes related to TreeFam can be access from SourceForge.net Subversion server at http://treesoft.svn.sourceforge.net/viewvc/treesoft/trunk/. Everyone can access Subversion server like this:
    svn co https://svn.sourceforge.net/svnroot/treesoft/trunk treesoft
In particular, TreeFam Perl API can be checked out by:
    svn co https://svn.sourceforge.net/svnroot/treesoft/trunk/tfscripts/Treefam Treefam
Documentations are available at http://www.treefam.org/api/.


Last Modified Tue Mar 6 09:39:24 2007 treefam@sanger.ac.uk