clustal alignment

marco12345

Member

Join Date: Mar 2013

Posts: 19
- Share
- Tweet
#1

clustal alignment

08-30-2013, 03:14 AM

Hi all,

I have to plan a little my work, and I have a question I am not finding answer.
How long could a clustal run be?

That would be using clustalw-2.1, and doing a multiple alignment on 10 fasta sequences of about 150 kb. The type of alignment is "slow/accurate", the ouput a PHYLIP file, and all the options are on default values.
I'm thinking on running it on a MacBook 3.1 with 4 Gb of RAM.

What do you think? Would that be too much for a laptop?

Thanks in advance.

Marco
Tags: alignement, clustal, clustalw, time
chuanchao

Junior Member

Join Date: Aug 2013

Posts: 3
- Share
- Tweet
#2

08-30-2013, 10:11 PM

why not use mega?
Comment
rhinoceros

Senior Member

Join Date: Apr 2013

Posts: 372
- Share
- Tweet
#3

08-31-2013, 04:05 AM

No, but I'd use muscle instead of clustal..

savetherhino.org
Comment
jimmybee

Senior Member

Join Date: Sep 2010

Posts: 119
- Share
- Tweet
#4

09-01-2013, 03:56 PM

From my experience with mitochondrial and chloroplast alignments, Id say less than a week. You could try Clustal-omeg. Im pretty sure its multi-threaded

Your laptop should handle it
Comment

Previous template Next

Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
Today, 05:17 AM
Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
07-01-2026, 11:43 AM
Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM

Topics	Statistics	Last Post
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, Today, 10:08 AM	0 responses 6 views 0 reactions	Last Post by SEQadmin2 Today, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, Yesterday, 11:05 AM	0 responses 7 views 0 reactions	Last Post by SEQadmin2 Yesterday, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 30 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, 06-30-2026, 05:37 AM	0 responses 28 views 0 reactions	Last Post by SEQadmin2 06-30-2026, 05:37 AM

Unconfigured Ad

Comment

Comment

Comment

Latest Articles

ad_right_rmr

News