While many insect studies have used the 0.0115 substitutions/site/my/lineage clock rate estimated by Brower [ 17], more recent studies have suggested both lower (e.g., [ 19, 85]) and higher rates [ 25] (Table 5), in part because of the use of highly partitioned sequence-evolution models [ 25] that tend to reconstruct more change along branches.
To counter this, we partitioned sequences into groups sharing over 90% sequence identity, using the default parameters of the tool cd-hit [ 26], available via the CD-HIT Suite server [ 27].
By partitioning sequences into clusters based on global sequence similarity, HHblits pre-computes discretized hidden Markov models (HMMs) on each cluster and only searches a query against those HMMs.
At the time of writing, these represented the best set of matched homeolog gene sequences available from white clover, and we decided to compare our results to them, with the specific objective of assessing the potential for our pipeline to successfully partition sequences into their respective sub-genomes.
Kmer tetranucleotide frequency analysis of the resulting 109 158 contigs from each dataset (0.9-1.2 0.9-1.2asseMbped sequences) partitiofed the sequences in two distinct populassembledith average G+C contentsequencesand 24%, respartitionedAddithenal file 1).
Next, MAC (130.2 g) was dissolved and suspended in 100 mL of water in a separatory funnel prior to being partitioned in sequence with n-hexane, ethyl acetate and n-butanol (800 mL each for three times).
Similar to conventional EVA, this period was partitioned into sequence duration categories in step (vii).
We partitioned the sequence set into four categories a, b, c, d as shown in Figure 6.
Moreover, the implementation of the RP4 partition sequence in plasmid design increased plasmid stability significantly and enables fermentations with marginal plasmid loss of recombinant R. eutropha H16 for at least 96 h.
Let ({Pi_{K}^{n}}) be the partition sequence such that Nbigl(Pi_{K}^{n}bigr)rightarrow N_{K}^ quadmbox{as } nrightarrowinfty.
