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This saves you valuable disk space but also time when loading the file into downstream analyses, such as Variant Calling or Differential Expression analysis, or into the Tablet genome browser.
Working with core labs that use structured naming conventions to track data for individual clients, we developed the Assemble by Name strategy that has become such a powerful and popular tool for combining multiple sequencing projects into a single analysis run.
Gene Codes has long been an innovator, investing in the R&D to develop powerful features for your DNA sequence analysis. Gene Codes developed the Assemble to Reference Sequence strategy that is widely used to speed up assembly and assign base-numbering systems and features to new data. The variance table was developed in the mid 1990's and became a key element first for forensic sequencing of mtDNA, and then for virtually all of our collaborators.
MUSCLE uses an iterative approach. This means that if you use it to create your MSA, the algorithm tries to correct alignments by repeatedly realigning the sequences as new ones are added.
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