We describe and assess the performance of the gene finding program pretty handy 
annotation tool (Phat) on sequence from the malaria parasite Plasmodium 
falciparum. Phat is based on a generalized hidden Markov model (GHMM) similar to 
the models used in GENSCAN, Genie and HMMgene. In a test set of 44 confirmed 
gene structures Phat achieves nucleotide-level sensitivity and specificity of 
greater than 95%, performing as well as the other P. falciparum gene finding 
programs Hexamer and GlimmerM. Phat is particularly useful for P. falciparum and 
other eukaryotes for which there are few gene finding programs available as it 
is distributed with code for retraining it on new organisms. Moreover, the full 
source code is freely available under the GNU General Public License, allowing 
for users to further develop and customize it.