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Multiple alignments based on CDK amino acid sequences were generated with MUSCLE [ 53] and then manually improved, yielding 226 amino acid positions (Additional file 6: Figure S3).
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The fragmentation of our new design is significantly improved, yielding more intense complementary ion signals, allowing complementary ion cluster analysis as well.
As the Arts Alliance's role has grown, its relationship with the state has improved, yielding almost $40,000 in grants in 1989-90.
In the second stage, the underlying guide-tree is iteratively improved, yielding a new progressive alignment.
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 alignment was manually improved when deemed necessary.
The resulting alignments were manually improved using the software bioedit 7.0.9 [ 33].
Multiple alignments were performed with Clustal W [ 41] and subsequently manually improved.
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.
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