Read pairs with either read alignment within an LTR were removed and the resulting set of filtered reads were assembled with Trinity [ 42, 43] using default settings.
Using all species, with either a concatenated protein alignment or a codon aware nucleotide alignment of all 65 genes, we constructed a robust phylogeny representing the likely relationships between the major plant parasitic nematode clades.
A slightly different topology again was found when the 3G dataset was analysed with MrBayes without RY encoding, either with the alignment partitioned by region or simply concatenated.
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Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd.
Moreover, we demonstrated the benefits of introducing hinges by showing the significant improvement in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd (on the DynDom dataset).
A sub-map alignment π1 is said to be conflicting with another alignment π2 if either: the sub-map of π 1 overlaps the sub-map of π 2; or π 1 aligns to the same in silico map as π 2, but in a different location or strand.
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For the other remaining cultivars in this group, the PCR products amplified with the Pina-D and Pinb-D primer sets were directly sequenced from both strands by SinoGenoMax Co., Ltd (http://www.sinogenomax.com/) and genotypes were confirmed by alignment with either known Puroindoline-D1 alleles or the NCBI blast website (http://blast.ncbi.nlm.nih.gov/).nih.gov/
We filtered out predicted variants with genotype quality scores lower than 40, falling into annotated repetitive regions (i.e., transposons, telomeres, centromeres), or falling into duplicated regions predicted either by reads with multiple alignments or by the CNVnator algorithm [ 23].
Therefore, our search process is constrained successively by an increasing score level K, starting from K=0 for an exact match, and ending either with a successful alignment at some K or at a maximum score level specified by the user.
