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May 17th, 2024: NPS@ updated (see NEWS).


KALIGN help

A brief introduction to KALIGN
Kalign is a progressive alignment method striking a good balance between accuracy and speed compared with other alignment programs on a range of popular benchmark datasets. Kalign program uses the unweighted pair group method with arithmetic mean (UPGMA) algorithm to construct a guide tree resulting in quadratic time complexity. More recent alignment programs have overcome this hurdle by implementing heuristics to construct guide trees. Kalign 3 is a completely re-written and updated version to meet current and future alignment challenges, introducing a SIMD (single instruction, multiple data) accelerated version of Gene Myers’ bit-parallel algorithm (Myers, 1999) to estimate pairwise sequence distances and adopting the sequence embedding strategy introduced by Blackshields et al. (2010) to speed up the construction of guide trees.

Availability in NPS@
KALIGN is available :

The set to align cannot have more than 1,000,000 characters.
So, for example, you can use KALIGN to align a set of similar sequences built from a BLAST search.

Parameters
The -super5 option is used for computation.
The output format is CLUSTAL W.

NPS@ KALIGN output example
The NPS@ KALIGN output is divided into three parts.

References


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