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In the case of A. albopictus sequences, our tuning experiments showed that two iterations performed on a data set with 0.1× coverage ensured the best assembly N50 and that supplementary iteration showed no significant improvement in the quality of the assembly (supplementary fig. S2, Supplementary Material online).
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Domain analysis of the sequences identified in five iterative HMM searches (jackHMMER) using the E. coli TamB protein (UniProt: P39321) as the initial search input, showed that the number of proteins containing the DUF490 domain characteristic for TamB (Selkrig et al. 2012), as well as the AsmA domain, each plateaued at the fifth iteration (supplementary fig. S1, Supplementary Material online).
The results from these programs are recycled to PONDEROSA for the next iteration (Supplementary Fig. S4).
For most chromosomes, the single base error detection drops to zero after the fifth iteration (Supplementary Table S1).
Convergence for gene expression datasets from E1 is usually achieved after 5 K iterations (Supplementary Fig. S2), and the posterior densities can be estimated from the RJMCMC traces of 75 K iterations, after the first 25 K iterations are discarded as burn-in.
A less strict mapping algorithm like BlastN maps 1 598 549 and 2 051 404 reads in the first and 10th iteration, respectively (Supplementary Material).
We discuss the relationship between gene tree accuracy and the number of local search iterations in Supplementary Section S4.
Excluding the most distant pair in each step results in smaller distances as the iterations proceed (supplementary table S3, Supplementary Material online).
To reconstruct the recombination maps of simulated data, we ran LDhelmet using a block penalty of 50 for 250,000 iterations after 50,000 iterations of burn-in (supplementary fig. S13, Supplementary Material online).
With our chosen occurrence and P-value thresholds, the final list of variables sees little change after ∼50 iterations (see plot in Supplementary Material).
Therefore, we compared the features extracted at each outer iteration of the double CV (Supplementary Figure 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com