This was incredibly useful and clear, you've really helped me to understand the links between the biology and visualization on the alignments (better than any of my MSc professors...) - thank you so much!
I could not change my txt document to fasta even if I have renamed and if I use MEGA to save the file, it just shows MAS format, not FASTA format. As I use MAS format file to align using MUSCLE, it shows error, how to overcome this problem?
Thank you so much for such an informative and constructive tutorial. Please I am looking for how to get SNPs, Allele frequency, heterozygosity and homozygosity.
Nice and clear, but please help me, I am trying to do a multiple alignment of sequences using Muscle but keeps getting an error "Stop codon(s) are found in the translated sequences. Please select a correct Genetic Code or coding frame." What am I missing?
Whenever I try to align a series of whole DNA sequences (from bacteria) the software keeps giving me an error message "MUSLCE log file did not end properly, suggesting an unhandled exception" and I am not sure what does that mean. I downloaded all my files from NCBI and they all are in .FASTA files.
hello nice turorial, well i have whole mitochondiral sequence of 300 individual, obtained from NCBI, and after trimming i am doing alignment and its though producigng more gap and increasing sits number from 15K to 21 K, is it ohk ?
Its a very good lecture ... dear sir if you can to make a lecture about SNPs detection and allele frequency from multiple genes sequences as well as how calculate hardy-weinberg equation, I will be very grateful from you ... thank you so much
Thank you for the topic suggestions. Yes, I can do that - those are all important. I will break those into several videos and over the next month or two.
I see a lot of articles include the alignment in their papers. How do you download that Mega sequence alignment and have it be in that same format they publish?
You first need to check what kind of alignment format they are using. With your own alignment open in MEGAX you can go to "Data" then "Export Alignment" and select the format you want. In MEGAX, the only options are MEGA, FASTA, and NEXUS/PAUP. If you need your alignment in a different format I would export it as FASTA and then search for a program to convert it to the one you want. Hope this helps.
This was incredibly useful and clear, you've really helped me to understand the links between the biology and visualization on the alignments (better than any of my MSc professors...) - thank you so much!
Glad it was helpful! Thanks!
Thanks. A video on sequence cleaning in Multiple sequence alignment is much appreciated.
Very useful for my Biology class, thank you!
Amazing! Thanks from Sweden :)
I could not change my txt document to fasta even if I have renamed and if I use MEGA to save the file, it just shows MAS format, not FASTA format. As I use MAS format file to align using MUSCLE, it shows error, how to overcome this problem?
Thank you so much for such an informative and constructive tutorial. Please I am looking for how to get SNPs, Allele frequency, heterozygosity and homozygosity.
Thank you for the lesson!
It is Showing error message, while I go with "Align DNA" using MUSCLE. How can I overcome that problem?
Nice and clear, but please help me, I am trying to do a multiple alignment of sequences using Muscle but keeps getting an error "Stop codon(s) are found in the translated sequences. Please select a correct Genetic Code or coding frame." What am I missing?
Does the DNA work for RNA sequences
Such a good tutorial!!!
Whenever I try to align a series of whole DNA sequences (from bacteria) the software keeps giving me an error message "MUSLCE log file did not end properly, suggesting an unhandled exception" and I am not sure what does that mean. I downloaded all my files from NCBI and they all are in .FASTA files.
Great video lecture! Can we have your tutorial on alignment trimming and editing? Thanks
Sure thing! Will try to get that up soon.
Thank you!
Thanks a lot.
hello nice turorial, well i have whole mitochondiral sequence of 300 individual, obtained from NCBI, and after trimming i am doing alignment and its though producigng more gap and increasing sits number from 15K to 21 K, is it ohk ?
Love it
How would you replicate this for 5 different genes at once? For example Cox1,2,3 cytb and RAG1 for a number of species?
Did you end up making a video on getting just the coding sequences?
Its a very good lecture ... dear sir if you can to make a lecture about SNPs detection and allele frequency from multiple genes sequences as well as how calculate hardy-weinberg equation, I will be very grateful from you ... thank you so much
Thank you for the topic suggestions. Yes, I can do that - those are all important. I will break those into several videos and over the next month or two.
Can you tell me how to make a partial selection instead of a full selection?plz
Mega software website is not loading...I had to download it..please help
i am not able to change type of my file🙂
I need at least 10 sequences how can i do ?
I see a lot of articles include the alignment in their papers. How do you download that Mega sequence alignment and have it be in that same format they publish?
You first need to check what kind of alignment format they are using. With your own alignment open in MEGAX you can go to "Data" then "Export Alignment" and select the format you want. In MEGAX, the only options are MEGA, FASTA, and NEXUS/PAUP. If you need your alignment in a different format I would export it as FASTA and then search for a program to convert it to the one you want. Hope this helps.
@@janeckagenomics2719 Thank you