Sentence examples for alignments were input from inspiring English sources

Truncated alignments were input to PhyML for phylogenetic analysis using the parameters described above.

All 5400 EST-like gappy alignments were masked with each of the 36 different combinations of variable REAP parameters and the resulting masked alignments were input to phylogenetic analyses as described below.

The value for each sequence alignment was input into the PHYLIP program, PROML.

The resulting alignment was input to PhyML for the construction of an Actinobacterial species tree.

A typical workflow is as follows: first, the alignment is input as a Stockholm or FASTA file.

Genomic sequencing reads from field isolates were first mapped to the genome of reference strain 70 15 with TE region masked, using SOAPaligner2 [ 51] and then the sorted alignment files were input into SOAPSnp [ 54] for SNP identification with parameter set as "r 0.0001 –t –u –L 76".

Once the optimal anchored target-template alignments were computed, these were input to the automated homology modeling script of Discovery Studio from Accelrys, Inc. (San Diego, CA) that uses standard force fields to determine the energy minimized 3-D structural coordinates for the test sequences, including those from recent CASP experiments (as illustrated by examples in Figure S7).

Alignment results (delta files) were input into "mummerplot" program to generate dot plots.

For median joining (MJ) network analyses, sequences previously aligned with Fluxus' DNA Alignment 1.121 software [ 31] were input in the program NETWORK 4.1 [ 31].

The program PAL2NAL [ 41] was used to convert the protein sequence alignment into the corresponding codon-based nucleotide alignment, which was input into the codeml program in PAML [ 42].

Sequence reads in the resultant alignment files are input into our RNA-Seq analysis, intersected with a BED file containing exons from the UCSC known genes reference table [ 13], and assigned to the overlapping gene.