Sentence examples for multiple alignments as from inspiring English sources

SSAP originally produced only pairwise alignments but has since been extended to multiple alignments as well.

Building on the Bio-SamTools distribution, ViennaNGS::Bam provides a set of convenience routines for rapid handling of BAM files, including filters for unique and multiple alignments as well as functionality for splitting BAM files by strand, thereby creating two strand-specific BAM files.

Given multiple alignments as input, the program estimates evolutionary parameters directly from these training data.

Bootstrap values were calculated using PhyML 3.0 (http://www.atgx-montpellier.fr/phyml/) the RAxML-generated trees with their corresponding multiple alignments as the initial input [65].

Protein secondary structure predictions were made with the JPRED program [ 53], using multiple alignments as queries.

Picasso [ 10] uses multiple alignments as profiles which are then merged hierarchically.

This seems to hold for classical progressive multiple alignment as well as statistical consistency alignment.

The Shannon entropy [37] was calculated for each position in the multiple

We confined ourselves to one sequence pair each from a multiple alignment as a basis for the substitution matrices (instead of considering all possible pairs) in order to avoid bias towards those proteins whose multiple alignments were constructed from many sequences [2].

Protein secondary structure was predicted using a multiple alignment as the input for the JPRED program.

Protein secondary structure was predicted using a multiple alignment as the input for the JPRED2 program.