The purpose of AutoTree is to automatically create alignments and phylogenetic trees for one or more amino acid sequences. AutoTree takes as input a FASTA file, containing one or more amino acid sequences. Using the algorithm described in the paper, AutoTree checks each sequence against a local installed non-redundant protein database, decides which homologues to use, checks SWISSPROT for additional homologues, retrieves the homologues, aligns the dataset and finally reconstructs a phylogenetic tree.


To generate all phylogenetic trees for the complete genome of Thermotoga maritima one would issue following commands:
     mkdir T.maritima
     cd T.maritima
     zcat BTM.pep.gz > thermotoga.aa
     nohup thermotoga.aa >& thermotoga.log &
Depending on the speed of your computer, this would take everything from a couple of hours (e.g. our IRIX machine) and a week (on my P300 Laptop).


Python, a local installed non-redundant protein database (SWISSPROT + TREMBL), gzip, clustalw, blast2.0, paup4*
Thomas Sicheritz <>
Last modified: Wed Jan 10 20:59:55 CET 2001