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Newly obtained EEF2 and HSP70 sequences were manually assembled and aligned to sequences downloaded from GenBank using MacClade ver. 4.08 [97].
After pre-processing, the data were manually assembled and aligned using CODONCODE CodonCode Corporationn, Dedham, MA).
Chromatographs were checked manually, assembled and edited using Bioedit 7.0.1 [ 90].
Sequences were manually assembled and aligned with BioEdit version 5.0.6 [ 27].
Therefore, we manually assembled and annotated all dynactin and actin-related sequences used in this study.
Two scaffolds, 26 and 45, could be manually assembled and were initially separated due to their short overlapping regions.
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As a reference tree for these 14 genomes, we used a tree based on a multiple sequence alignment of manually assembled CAP and Arp2/3 protein sequences as published by Hatje and Kollmar (2012).
These systems are manually assembled, expensive, and unreliable.
Sequences were checked manually, assembled, aligned, and annotated in Geneious Pro 5.4 [ 39].
The PCR products were directly sequenced in both directions, manually assembled, edited and aligned in MEGA 5 (Tamura et al. 2011).
Associations between genomic instability and Pathways, Gene Ontology and manually assembled gene lists were tested with R/bioconductor [30] and Webgestalt [31].
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