Sentence examples for used the command line from inspiring English sources

We used the command line version of MEME 4.0.0 (http://meme.sdsc.edu/meme4/meme-download.html ) compiled on a Linux machine.

We used the command line CLC bio Assembly Cell (Aarhus, Denmark) to generate an initial assembly due to the small memory footprint of this assembler.

In PSMC, we used the command line options -N25 -t15 -r5 -p "4 + 25*2 + 4 + 6" that have been successfully used in previous similar analyses of human and great apes [ 64].

Next, we used the command line version of PennCNV software that integrates, in a joint-calling algorithm, a Hidden Markov Model (HMM) with family relationships, signal intensities for parent-offspring trios, marker distance and population frequency of allele B [ 17].

We used the command line version of RNAsubopt with options "-ep 5 -p 1000 -noLP", which specify the percentage from the MFE (5%), random sample size (1000) and disable prediction of helices of length 1. RNAfold was used to compute partition function and base-pair probabilities.

Also, we used the command line version of cd-hit-454 (v. 4.6, Li and Godzik, 2006; Niu et al., 2010) to cluster our shotgun data at different stringency settings (between 91% and 100%), where 98% is the default stringency in cd-hit-454.

We used the command line-based coalescent simulator msms (Ewing and Hermisson 2010) to first simulate founder allele frequencies and then used them to simulate admixture proportions and genotypes of admixed individuals.

And to manage it, you simply rely on the regular AWS management console (or use the command line).

Column number 11 contains the sum of all time values, which is calculated by using the command line tool bc.

Additional file 1: Annex I. Building and using a QSAR model in eTOXlab using the command line interface; Annex II.

Thus, LBVS becomes straightforward for scientists who may not be comfortable with using the command line interface.