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However, situations do exist for which the first two methods are preferred and using the FASTA method could be dangerous.
When using the FASTA method, underestimating heritability was actually more risky (in terms of type 1 error rate and power) than overestimating it.
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Local alignment of protein sequences was done using the FASTA suite (http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml).shtml
The orthologue relationships were determined by best-best hit analyses using the FASTA package [87] on a desk-top computer.
The percentages of similarity were determined using the FASTA network service (European Bioinformatics Institute Fasta Service; available from http://www.ebi.ac.uk/fasta).ac.uk/fasta
Identities were determined by the EBI (European Bioinformatics Institute) using the Fasta 3 network service [ 57].
Therefore, it appears that the fasta method works regardless of which estimate of heritability is used.
Power was always lower with the GRAMMAR method than with the fasta METHOD.
In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.
The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate.
The resulted FASTA files were imported in MEGA4 and pairwise distances were calculated using the Pamilo Bianchi Li method (Pamilo and Bianchi 1993; Tamura et al. 2007).
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