Sequences in each amino acid sequence dataset were aligned by using ClustalW version 2.0.12 (21 ).
The sequences in each dataset were aligned by using the computer program ClustalW version 2.0.12 (24 ).
Each dataset was aligned by Muscle [38] first and further adjusted manually in Bioedit [39].
When the full dataset was aligned by DIALIGN, 67% of aligned blocks split into an average 3.5 fragments, and 86% of blocks were co-aligned on average with 1.7 others.
Then contigs of both datasets were aligned on reference chromosomes of TAIR10 assembly by BLAT.
The simulated reads generated by the wgsim package (see section " Datasets") were aligned to the simulated reference genome using novoalign [ 13].
All datasets were aligned using CLUSTALW 1.82 [ 72] with default alignment parameters.
The sequences from the remaining datasets were aligned with ClustalX as above, with no sites excluded.
Individual datasets were aligned using a minimum of four reference samples from each participating lab.
The individual MS imaging datasets were aligned to each other.
