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Partial deletion constructs were named according to the omitted sequence.
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We then omitted sequences that are shorter than 100 bp from the design process.
We omitted sequences with a Z score > 2 in an alignment, that is, those with larger deviations in composition, from a concatenation of 59 ribosomal proteins.
The coordinates of the omitted sequences (labelled DUPL A-E) are provided in Additional File 1 for reference, but we believe there is insufficient evidence of their validity to warrant their inclusion in the present analysis.
Some of the omitted sequences are highly repetitive sequence reads, others may have enough sequencing errors that they did not match the assembled sequences, others are assembled sequence contigs that appear to be duplicates of sequences in the assembly (perhaps from the second haplotype).
Analyses omit sequence positions containing a gap and do not include insertion deletion polymorphism.
The assembled transcripts were filtered to omit sequences < 200 nucleotides.
(b) As in (a), but also omitting sequences from lampreys.
Sequences were quality trimmed from the 3' end using Trimmomatic 0.32 [ 43], omitting sequences where the average quality scores in sliding windows of 5 bp dropped below 20.
However, no investigations have gone beyond the hydromedusan and ctenophoran representatives, potentially obscuring the evolutionary history of this gene family by omitting sequences from other phyla.
aeolicus Nankai 3. The former failed on 28 sequences, whereas the latter failed on 43, so the outgroup was constructed using two representatives from Nanohaloarchaea and one from Methanosarcina, omitting sequences that failed the compositional homogeneity test.
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