For the remaining datasets of BAliBASE, all consistency-based programs, namely Probcons, T-Coffee, Probalign and MAFFT still produced alignments with higher accuracy when compared to the other five programs.
In this research, we use one month data for building the model and the remaining dataset (20 days) for the testing.
The remaining dataset is used for fitting more models when possible.
For the remaining dataset (HBV5), resolutions of the PRF processed structure and the structure generated by Orig-EMAN were almost the same.
For the remaining dataset, 1,632 japonica and 455 indica cDNAs, as well as 47,549 japonica and 12,934 indica ESTs have been mapped to multiple locations, implying the results of genome duplication events or the relics of pseudogenes [ 31].
Sensitivity analyses performed by sequentially removing each study and reanalysing the remaining dataset (producing a new analysis for each study removed) did not lead to major changes in direction or magnitude of statistical findings.
Sensitivity analyses were performed by sequentially removing each study and reanalysing the remaining dataset (producing a new analysis for each study removed) and by analysing only data from studies with low risk of bias.
The training datasets for each of these runs were composed of four of our five datasets (SLO, NOV, KAT, SAE, SIR) and the remaining dataset was used as the test dataset (leave-one-out scheme).
No evidence for isolation by distance was detected for the remaining datasets: (i) Cyt b modern samples, (ii) Cyt b ancient samples, (iii) Cyt b modern+ancient samples combined, (v) control region ancient samples, (vi) control region modern+ancient samples combined, and (vii) Cyt b and control region combined for ancient samples.
For the remaining datasets, raw data were downloaded from the GEO or Array Express databases and normalized with BRB Array Tools v3.7.0b1 developed by Dr. Richard Simon.
