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The alignment was manually improved when deemed necessary.
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Gene duplicate pairs and their associated outgroup sequences were first aligned with ClustalW 2.0 and then manually checked and improved, when necessary, before the analysis.
To evaluate some of the secondary phenotype predictions, we manually investigated some of the cases were the predictability of known disease genes improved when adding the predicted secondary phenotypes.
The initial model was automatically built with ARP/wARP [24] and manually improved using the program COOT [25].
Sequences were assembled with IDBA-UD (2 ) and manually improved.
The resulting alignments were manually improved using the software bioedit 7.0.9 [ 33].
Before determining intron loss or gain, some alignments were manually improved.
Multiple alignments were performed with Muscle 3.6 software [ 67] and were subsequently manually improved.
Multiple alignments were performed with Clustal W [ 41] and subsequently manually improved.
The resulting model was manually improved in Coot[ 52] and refined with phenix.refine (PHENIX).
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