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However the lower 0.025 posterior distribution value of the pairwise migration estimates (M) never differed from 0. In other words, migration rates between populations never differed significantly from zero, and the direction of gene flow between sampling locations could not be inferred using this approach (results not shown).
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Finally, 3,985 interlogs were inferred using this approach, and the total number of interactions including source and inferred interactions were 5,509; 2,323; 524; 599 and 134 for human, mouse, sea urchin, fruitfly, and coral, respectively (see Additional files 7, 8, 9, 10, and 11).
This can be inferred using the neighbor-joining method (Tamura and Nei 1993).
Haplotypes will be inferred using the PHASE software package [ 97].
Finally, maximum likelihood distance matrices were inferred using the model specifications from jModelTest; this was done with PUZZLE [ 22].
This tree was inferred using the same set of concatenated genes used for constructing the species tree but now inference was done based on the nucleotide sequences.
Homology relationships across all genomes analyzed in this study were inferred using the Orthologous MAtrix algorithm (OMA) [ 46] with the following default criteria: alignment length > 60% of the minimum gene length and alignment score > 181 in Gonnet PAM matrix units.
Haplotypes will be inferred using a Bayesian method (PHASE).
The evolutionary relationships were inferred using the neighbor-joining method.
Orthologs are inferred using the Reciprocal Smallest Distance algorithm.
The phylogeny was inferred using the Maximum Parsimony method as described in the methods.
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