Sentence examples for methods with default from inspiring English sources

Three ML methods with default settings applied in this web were used: SLAC, REL, and FEL.

The following methods (with default options) were used: RDP, Chimaera, BootScan, 3Seq, GeneConv, MaxChi, and SiScan.

ADMIRE was invoked from the web interface using a custom sample-definition file (see " Methods") with default parameters.

We also notice that relying on semantic similarity networks constructed using the other methods (with default threshold values) yields similar results as we analyzed above (Table 2).

The chromPETs were mapped back to the current reference genome assembly (hg19) using Novoalign (see Materials and Methods) with default parameters.

Phylogenetic analyses on aligned sequences were performed using PHYLIP version 3.69 [ 35], using the maximum parsimony (100 replicates, 10 jumbles), maximum likelihood without the assumption of a molecular clock (1,000 replicates, 10 jumbles) and neighbor-joining (1,000 replicates) methods with default parameters.

The MEGA5 program using the Neighbor-Joining method with default parameters besides 1000 bootstrap replications was used to generate the phylogenetic tree (Tamura et al. 2011), which was further edited by using the Interactive Tree of Life on line tool (iTOL, http://itol.embl.de) (Letunic and Bork 2016).

Normalization was done using the ranking-mode method, with default value for any parameter.

Phylogenetic trees for the LTRs were built using the PhyML software, using HKY+G and GTR+G substitution models [25] under the maximum likelihood method, with default parameter values and 1000 bootstrap replicates.

To assemble the SNP tags, we used bwa software with "aln" method with default set up.

De novo assembly was performed using the Trinity method with default parameters [ 58].