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Genomic data for conducting the blastp searches were obtained from the following locations: Neurospora genome data (version 7) was obtained from the Broad Institute [ 36, 37].
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The instruction file for the ratchet searches was obtained using the Perl script perlRat.pl v1.1.
Articles resulting from a comprehensive electronic search were obtained, their references examined, and all other relevant articles not already discovered via the electronic search were acquired and reviewed.
Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value.
Initial trees for the heuristic search were obtained automatically by applying neighbour-join and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood approach and then selecting the topology with superior log likelihood value.
Initial tree(s) for the heuristic search were obtained automatically as follows.
Relevant stacks for promoter search were obtained from the primary transcript enriched sequencing library.
The initial trees for the heuristic search were obtained automatically as follows.
Initial tree(s) for the heuristic search were obtained automatically as following.
Initial trees for the heuristic search were obtained automatically with MEGA 5.
Initial tree(s) for the heuristic search were obtained automatically as described above.
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