Hi,

I have been using Ugene for the first time today,
After watching some videos and reading the manual i got started to make an aligment with some DNA sequences of a bacteria.

I have 15 DNA sequencies whiche are all around 4.4M Nucleotides.
I have been able to align them in an .aln file.

When i want to alignmen them using Kalign or ClustalW they are able to start. i don't get an error when i want to align them.

How ever they keep stuck at 14%(when using Cluster) and 75%(when uding Kalign). When i use less sequences i keep getting the same results.

I am using W7 64 Bit and i am using the 64 bit full version of the program.

I have 8GB of RAM and have appointed 6GB to the program.
Increasing or decreasing doesn't influence the result.

When i run the program it doesn't consume more then 2GB of my RAM and the activity of my CPU cores(have 4) are all around 80-90%.

Another thing is that when i start the alignment they get at 14% and 75% really quick and then remain stuck there for a few hours( 2 hours when i am typing this).

I hope you guys can give me any advice for helping this issue.

greeting
Covux

Yuriy,

Thank you for your answer i'll look into those programs.

Will one of those programs be integrated in the verison that will be releases this month?

I have a other question:

is it somehow possilbe to look for STR in more then 1 aligment at the time.

When i have one sequence i can look for STR, but i want to look for STR in more then one aligment so i can sport diffrences in length very fast.
Is this possible?

Covux