Good to hear from you, and I'm happy my video helped you understanding what is 16S rDNA😊

Glad it was helpful! 😊🧡

Hello, for DNA precipitation you can incubate your samples at -70 degrees celsius overnight.

Thank you

send me an email, [email protected]

Welcome😊

Hello! I'm from the Philippines 😊

Thanks 😊

You're welcome 😊

Hello, please send me a message through my messenger- Madison Munar

Hello, please send me a message through my messenger- Madison Munar

Thank you😊

hi, do you have specific concerns regarding the phylogenetics analysis? please let me know☺️

Hi @sunflower5990, if the bootstrap value is below 50% the grouping is not well supported, you may check your alignment if there are gaps and unaligned sequences, all the best!😊

Hi @nurtenyilmaz430, for phylogenetics analysis using the MEGA software you can watch this video 👉 kzbin.info/www/bejne/govZin-PrZdsipI, if you have questions, please feel free to comment, all the best! 😊

Thanks 😊

Hello, please send me email at [email protected]

You're welcome! 😊

Awesome, you're welcome and thank you! 😊

You're welcome 😊

Hi @sumnilmarwa4519 , make sure your aligned sequences have the same lengths and direction

Hi @aannajarvis4188, you need to build three cladograms using three different building methods, then compare the clustering of the samples, if the three cladograms agree then most probably the analysis of your samples is correct and is highly supported, you can choose any of the three cladogram to use for presentation, all the best!

Hi @mikeoduor1327 ! I think CodonCode Aligner will be of big help in the assembly of your DNA sequences (forward and reverse DNA sequences) after quality trimming where you need to trim ambiguous reads based on the quality of chromatogram results, you should do the proofreading and quality trimming prior to its assembly to ensure that only high quality reads are included in the analysis, furthermore, most of the times primer sequences both forward and reverse would still be present after the quality trimming of low base reads, hope I answered your concern about using the sequence as it is, short answer is no, since low and erroneous base reads are still present in the raw DNA sequences and must be trimmed/cut prior to its assembly, it's the so called "garbage in garbage out" in bioinformatics analysis, you need to use high quality data/sequence in order to get high quality and credible results, all the best!😊

Hi Amany, although enzymes are just one kind of the proteins that maybe produced from a specific gene after translation, every gene encoded in the DNA codes for a specific protein

Hi Ozgun, I have another video for the result interpretation 👉 kzbin.info/www/bejne/h52wqIang8d-d5o

Hi Azi, you're welcome, please send me message through my messenger

You're welcome 😊

Hello Kinkpe Lionel, sure please send me a message through my messenger (Madison Munar)

Hi Ashwini, sure just send me your cladogram maybe through my messenger. Provide a simple objective so I may know what to look at the tree.

Hi, sometimes the program may suddenly crash due to low memory storage of the computer, or the data in the samples being analyzed is too big.

Hi Soussou Darine, usually we can only build a cladogram which infers evolutionary relationship among the samples being analyzed, including an outgroup can provide a sense of root or evolutionary origin which is being reflected on a phylogenetic tree, however, the tree is only an inference since the outgroup is not a definitive root of the organisms under study

You can read this protocol on lipid extraction from plants 👉 currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cppb.20114

Thanks 😊

@@MadisonMunarPhD Sir, I have a few doubts, How can i contact you

@@chetanhiremath4941 send me a message through my Messenger- Madison Munar

Hello Joanna, sometimes this error usually occurs due to the shortage of memory to store the data. You may check the available memory on your computer.

Hi JC, yes Neighbor-Joining and Maximum Likelihhod, usually would show a scale bar for estimation of sequence divergence, I suggest to create or test at least three (3) building methods and compare the formation of the clades, if all 3 different building methods agrees then most likely the analysis is correct.

@@MadisonMunarPhD Thanks for reply. I have encountered a problem that the max likelihood tree that I have constructed didn’t show the scale bar after I selected the “Topology Only” tab. Does it means that it is not possible to show a scale bar in the max likelihood tree unless we deselect the “Topology only” tab ?

Hi Vinothini, you need at least 5 sequence samples in order to perform the alignment, if this is not the case, you may try to uninstall the program and reinstall, then try to use the same sequences for alignment

Thank you for your reply. I have 37 sequences but got error.I will do your suggestion.

Hello Yokai, yes that's right, you can have a BLAST analysis of your 16S rRNA sequences and you may opt to include 10 organisms in your phylogenetic analysis. I have also a video on how to do proofreading and quality trimming of raw DNA sequences 👉kzbin.info/www/bejne/nWqYZZudjsp_h68, and DNA sequence assembly 👉kzbin.info/www/bejne/e5rbiWZmr999eac, all the best😊

@@MadisonMunarPhD Thank you for your answer, if you do not mind, i have another question regarding Bootstrap values. what does it mean when a branch does not have a bootstrap value?

thanks😊

@@MadisonMunarPhD Most welcome

thanks😊

Hello Kashish, you may observe sequence inversions by visually checking your alignment, I usually include duplicates of the same sequence for control.

@@MadisonMunarPhD actually m confused in identifying in the alignment . Btw thanks 😊

Hi Emi, I hope I can take a look at your cladogram for me to evaluate it, however, based on your question, it seems you are using different accession numbers for the same species which leads to a slightly different tree everytime, I would suggest that you check the information about the sequence by clicking on the Accession Number, make sure that the reported sequences are the same, for instance if the two species with different Accession Numbers were both 16S rDNA sequence, if the DNA sequence reported were different most probably it will not be aligned thus will be interpreted as a different species. So make sure you are using the same DNA sequence or gene in your phylogenetic analysis.

@@MadisonMunarPhD thank you very much for your reply and explanation sir. Yes, they both are the same tufA sequence, and its make me confused. Do you know any journal or book that I can read for understanding this topic sir? thank you

Hello again Emi, if it's the same gene I also wonder why it makes a different tree, you may also check the direction of the sequences, you can simply observe the alignment and if the two similar DNA sequence were not exactly aligned most probably their direction is different, you can change the direction of the sequence by clicking "DATA" then "REVERSE", this will change the direction of the sequence.

@@MadisonMunarPhD thank you very much sir, I've got a lot of information from you.

welcome, good to hear from you Emi😊

thanks😊

Hello Sufyan, thanks😊 👉download SnapGene Software (www.snapgene.com/) to be able to view the saved MSA and save into PDF file. Save your MSA in FASTA format in your desktop and then open using the SnapGene Software, open print preview and save in PDF format😊

thanks😊