how to align sequences in multifasta

Question

[goatsrunfaster]

Hi,

I have a multifasta with 14 sequences. The sequences are from 14 different isolates, but they are all the same gene.

Four of them are the + strand and the other ten are the - strand (which I believe means they oriented differently).

What is the best tool to properly align these sequences and make a NJ tree?

Any help is appreciated!

[GenoMax]

If you need to use a graphical program then MEGA is a good option on PC/Mac.

Answer 1

[lieven.sterck]

any multiple alignment tool should do I think. Eg. Muscle, emma, clustal-omega, ...

you do have to make sure that all sequences are in the same order in the fasta file (most commonly 5'-3' , so start to stop )