PhyloGenie is a PERL script combining the various steps necessary to producing a phylome. BLAST or PSIBLAST searches are performed for all FASTA format sequences in an input file, the HSP’s corresponding to user defined selection criteria (E-value, coverage, score per column, identity) are extracted and used as a basis for multiple sequence alignment. Phylogenies can then be infered using the supplied standard NJ method or any other program accepting aligned FASTA sequences as input and generating Newick format trees. As analysis of phylogenies is far more complex than analysis of BLAST results we also provide a tool to filter a set of phylogenetic trees for those corresponding to user defined topological selection criteria.
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Frickey T., Lupas A.N., (2004)
PhyloGenie: automated phylome generation and analysis.
Nucleic Acids Res., 32(17): 5231-8.