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Local LD analysis on SBI-06 used the full matrix option in TASSEL.
Similarity matrices were calculated using the similarity matrix option in the neighbour joining field of the arb software package.
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However, we also created 'generalist' states for species that utilize multiple plant taxa and then used the step-matrix option in Mesquite to define the cost to these states, from the plant taxa that are included within the generalist host range, as being zero.
The vertebrate binding matrices and the only high quality matrix option were used in the profile selection, and the cut-offs for core and matrix similarity were set to 0.9999 and 0.7 respectively without any change in the other options.
Protein distance for each pair of orthologs was calculated using Protdist in Phylip 3.69 (33) with the Dayhoff PAM matrix option.
(The rate-2/3 code and the rate-3/4 code are constructed using base-matrix option A in [2].) The performance of TDMP decoding is evaluated for each code with the Storm-1 processor using its 8-bit mode for saturating, fixed-point arithmetic.
A concatenated data set (generated with the fused matrix export option in Mesquite and using only individuals for which at least 2 loci were fully sequenced, with missing information coded distinctly from gapped characters) was evaluated for similar performance.
We created spatial interpolations of the Q matrix using the option in TESS to generate posterior predictive maps of admixture proportions.
We assumed that the working correlation matrix is independent, therefore: Using GEEs with the independent correlation matrix corresponds to exploiting cluster option in General Linear Models (in our case, cluster is a set of the particular patient's records).
Group participants were provided with a matrix listing the range of options and were asked to systematically compare each option with every other option in the matrix.
In recent years, the use of acellular dermal matrix (ADM) has emerged as an alternative option in the treatment of selected cases with extremity ulcerations [ 8].
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