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Alignment Overview

DECIPHER is excellent at quickly aligning thousands of input sequences while maintaining high accuracy. The examples below illustrate how to obtain accuracy and scalability for a variety of common alignment scenarios.

Why use DECIPHER for alignment?

  • AlignSeqs was the best out of 30 aligners on the extensive QuantTest2 protein benchmark.
  • AlignSeqs was one of the most scalable and accurate aligners on the RNAconTest ncRNA benchmark.
  • DECIPHER's multiple sequence alignment functions maintain accuracy better than other programs for larger numbers of input sequences.
  • DECIPHER uses secondary structure to improve alignment accuracy.
  • AlignTranslation makes it easy to accurately align protein coding (nucleotide) sequences.
  • AlignSynteny can align the syntenic regions of whole genomes.
  • All alignment functions are fast and scalable thanks to their use of anchoring and adaptive banding.


Align Sequences - Accurately align thousands of unaligned DNA, RNA, or amino acid (AA) sequences.

AlignSeqs



Align Translation - Using a set of protein coding sequences, create a nucleotide or amino acid alignment by aligning their corresponding proteins.

AlignTranslation



Align Synteny - Beginning from completed or draft genomes, find shared syntenic regions and align them quickly while accounting for inversions, rearrangements, and duplications.

AlignSynteny



Align Profiles - Efficiently create a merged alignment from two sub-alignments that may contain millions of sequences.

AlignProfiles



Align Pairs - Rapidly align pairs of nucleotide or amino acid sequences.

AlignPairs