In addition, in Bowtie 2 alignments, options were set to report all alignments instead of in the previous experiment when the BWA default parameters were used (report first three alignments).
First, four alignment algorithms, BWA-short [ 32], BWA-long [ 33], SSAHA [ 34], and Super-maximal Exact Matching [ 35] we employed to identify a list of Candidate Mapping Locations (CMLs).
We used the STAMP platform for computing the first five alignment-dependent metrics scores http://www.benoslab.pitt.edu/stamp/, the Mosta package included in SABINE for computing the AC scores http://www.ra.cs.uni-tuebingen.de/software/SABINE/downloads/index.htm, and the web server of KFV for computing the KFV scores http://bioinfo.uncc.edu/kfv/.
Thus, the correct alignment of M2 and M3 will be inconsistent with the first two pairwise alignments.
Subsequently, four different tree reconstruction strategies were applied on these two alignments: First, ML trees were derived as described above, using LG [ 56], since this model best fit 50 out of 53 of the individual alignments.
As for coverage rate (CR), UEDAMAlignKnownComplex and UEDAMAlignCoach also possess the first and the second best coverage rate in the two alignments.
The alignments in the first two classes were further processed using the Alpheus pipeline (Miller et al. 2008) for deriving per-gene read counts and sequence polymorphism calls.
We first defined codon positions in our two alignments using MacClade v4.07 [ 39] and then assigned the best model based on AIC scores calculated by jModelTest v0.1 [ 40] to each gene's codon sites in BEAUti v1.7.1 [ 38].
Here, we present, in more detail, two alignments (Table 1): first, zebrafish/Xenopus, which illustrates a best case scenario of two consistent ontologies, conforming to the CARO standards (Haendel et al., 2008), with annotations of synonyms and definitions, and low redundancy.
The first two parameters constrain the quality of alignment while the third parameter loosens the constraint to account for insufficient trimming or bad quality bases in the end of contigs, which are likely sequencing errors.
