Poorly aligned regions were removed from the alignment using GBLOCKs with the minimum length of a block set to 5 and no gap positions were allowed.
Poorly aligned sequences were manually removed from the alignment.
First, raw reads were aligned to hg19, and then PCR duplicates were removed from the alignment.
Allelic amino acid sequences were aligned and each site containing a gap was removed from the alignment (indel sites are illustrated in Additional file 1).
When more than half of the aligned sequences carried a gap at a given position, these positions were removed from the alignment.
The mature protein sequences were aligned with Cluster X version 2.0 and gaps were removed from the alignment.
Ambiguous regions and all sites including a gap were removed from the alignment.
Resolving strain relationships may improve if regions of recombination were removed from the alignment blocks.
Columns containing gaps as well as immediately adjacent columns were removed from the alignment before tree construction.
Gap-containing sites were removed from the alignment and Maximum Likelihood trees were inferred using ProML from the PHYLIP package (http://evolution.genetics.washington.edu/phylip.html) [78].
When Syagrus and Lytocaryum were removed from the alignment, Cocos resolved as the first branch after the African clade and thus sister to the remaining American Attaleinae.
