Sequencing technologies have improved significantly in the past 10 years and the staggering number of genome sequences available has led to a migration from single-gene phylogenetics to multigene phylogenetics. A protocol was developed here to compare fungal genomes through BLAST to determine which BLAST statistics may best represent phylogenetic information. The results suggested that levels of sequence identity, relative to the query length, may be useful for predicting whether a gene will yield a well-resolved and consistent tree. Moreover, it was found that about 40% of the genes in a typical filamentous fungal genome may lead to a well-resolved and concordant tree topology that also matched an 18S rDNA derived topology; but for consistent results, multigene trees with a minimum of five genes should be used. An additional script to rapidly identify regions within genes that can be easily amplified was then developed and tested on eight genes. The genes were successfully amplified and several resultant amplicon trees matched the 18S rDNA topology. / NSERC