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In our tetraspanin dataset, duplication branches produced by 2R-WGD are so ancient and divergent that they have much higher chance to suffer from saturation and model violation than speciation branches.
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Second, in the UP dataset some duplications could have occurred very recently.
For random datasets where duplications to the left and to the right occur in an equal rate, it is expected that the distribution of E n is close to the Gaussian distribution centered around the value zero.
This method of partitioning the dataset prevented accidental duplication of MOTU assignments across separate jMOTU runs.
The technical redundancy in the dataset (perfect sequence duplication) was removed using the NCBI nrdb program, included in the downloadable Blast suite.
The remaining LSG non-LSG paraLSG non-LSGfound in syntelog grouparalogare not linked to any of the three WGD events identified in the Bower et al dataset therefore indicating dupairstion events which are independent ofound.
The Arabidopsis thaliana α-duplication dataset contains a number of genes that have more than one duplicate due to subsequent gene duplications.
Furthermore, AtC3H12 and AtC3H28 were listed as duplicated genes in the segmental duplications dataset maintained from TIGR.
Phylogenetic analysis of a comprehensive ciliate dataset shows several duplications within ciliates, all of which are inparalogues (additional file 5).
To analyze the primary datasets for gene duplication and alternative splicing all non-perfectly matching EST sequences were removed from the EST assembly.
To detect directional bias, WAMI invokes ARLEM three times on the dataset: 1) with both duplication directions allowed, 2) with only left-to-right duplications allowed, and 3) with only right-to-left duplications allowed.
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