Question: Get pairwise scores from alignment without re-aligning?
0
gravatar for mpd
2.4 years ago by
mpd0
mpd0 wrote:

Hi there,

I'm looking for a way to extract pairwise bit scores from a multiple sequence alignment without realigning the sequences. Typical scenario is an MSA of around 1000 sequences, produced using MAFFT. I wish to obtain a bit score for each pair of sequences.

Currently I can do this manually by cycling through each sequence and comparing it with each other sequence, but this is slow and I'm sure there must be a quicker way out there, or a method of producing a MSA which outputs the scores. MAFFT --distout is not useful for my purposes.

Any ideas appreciated!

Thanks!

ADD COMMENTlink written 2.4 years ago by mpd0

Why is --distout not useful for your purpose?

ADD REPLYlink written 2.4 years ago by Joseph Hughes2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 881 users visited in the last hour