Blog

What is the best multiple alignment program?What is the best multiple alignment program?

How do I align multiple sequence alignments in the MUSCLE algorithm?How do I align multiple sequence alignments in the MUSCLE algorithm?

A fundamental step in the MUSCLE algorithm is aligning two multiple sequence alignments. This operation is sometimes called "profile-profile alignment". If you have two existing alignments of related sequences you can use the profile option of MUSCLE to align those two sequences.

How do I ask muscle to improve an alignment?How do I ask muscle to improve an alignment?

You can ask muscle to try to improve an existing alignment by using the – refine option. The input file must then be a FASTA file containing an alignment. All sequences must be of equal length, gaps can be specified using dots "." or dashes "–".

What is the –profile option in the MUSCLE algorithm?What is the –profile option in the MUSCLE algorithm?

A fundamental step in the MUSCLE algorithm is aligning two multiple sequence alignments. This operation is sometimes called "profile-profile alignment". If you have two existing alignments of related sequences you can use the –profile option of MUSCLE to align those two sequences. Typical usage is:

image-What is the best multiple alignment program?What is the best multiple alignment program?
image-What is the best multiple alignment program?What is the best multiple alignment program?
Share this Post: