Thank you Md Shaminur Rahman. Actually this my first time trying alignment and phylogenetic tree construction. I ran a CLUSTLW alignment on my query sequences at 6 am today by using MEGA. It is 2.31 pm and still its on going. Is it a normal processing time for MSA with larger sequences?

MEGA software with all its available version can do that

Dr. Zahra Al-Khafaji. I tried doing it on MEGA. When I run alignment with MUSCLE, it shows due to with insufficient memory. I exceeded memory usage to 4000mb as my system is of 8 gigs. Still it shows the same. I also run the alignment on CLUSTLW in MEGA on 6 am today. They alignment is still on process. Is it normal for the alignment to take that much of time?

Thanks a lot. It was really helpful.

I would suggest using MAFFT as suggested by Md. Shaminur Rahman

We have successfully aligned >17,000 SARS-CoV-2 genome sequences and it took 14min. Check out our paper below

Article Presence of mismatches between diagnostic PCR assays and cor...

Thanks Kashif Aziz Khan for the suggestion.

I made a phylogenetic tree of 200 genome sequences by using MEGA. It took almost 5 hours.

@Syeda Farjana Haque

What was your BP length of sequence?

@Md Adnan Karim

Each has 30kb.

@Syeda Farjana Hoque

Thanks a lot for the information. However, may I ask what Algorithm you used for the alignment? MUSCLE or CLUSTALW?

@Md Adnan Karim

CLUSTALW

For large sequences, you should use MUSCLE in the command line and preferably in a Linux operating system. Install MUSCLE via conda.

use the following command for allignment:

muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv

the documentation might help

http://www.drive5.com/muscle/muscle.html

@Syeda Farjana Hoque

Thanks a lot for your help. I also used CLUSTALW. it took me around 1 days. But later i used bioconductor package of R. It completed the task in less then 2 hours. All the scripts required are available online.

Md Adnan Karim That's great. I will try it. Thank you.

Md Adnan Karim Let me add my 2 cents from a computational perspective, See if you can batch process, instead of loading the whole sequence at one go, load it in batches. That way, the computation as well as analysis will be fast.

@Syed Hasib Akhter Faruqui

Thanks a lot for the assist. I will give it a try.

You can use MEGA-X software muscle programme. This tool take high load and give output in short time duration.

@Md Adnan karim

Is it normal to align by clustal-omega in R bioconductor and takes more than 24 hours and still running till now for 600 dna covid sequences with length almost 30000 characters. I know mafft is the fastest but most of related work in research papers clarified that clustal- omega can align >50000 seq in few hours how this happen?

Hi, I have around 10 Lakh sequence for alignment. May I know which software can be used? I tried with MEGA 11. After alignment, I couldn't open the .msa file.