Hi, may I ask why I click insert sequence from file, and I used the sample from the google drive (U94922 misson file), its not working.. it says the mega cant read the sequence
This was soooo helpful for an assignment I was stuck in because MEGA kept rejecting the sequences I aligned on ClustalX!!!!!!!!!!!!!!!!!!!!! YOU ARE A LIFE-SAVER HONESTLY THANK YOU SO MUCH!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Of course, you or I will not have the pre-loaded phylogentic tree file with the 5 other kinds of Kluyveromyces partial ribosomal genes waiting to be added in "edit". And they are extremely hard to search for in NCBI. (the Accession numbers in the screenshot aren't very helpful. BUT the GI numbers like 31581082, 4038945 etc (at the left of the species ID in MEGA) are. So, tediously search for each of those, send it to a FASTA file, and insert each of those files into MEGA. Sigh. Also, the automated open in MEGA on download thing seems to be a Mac "feature" and super dangerous. If on another kind of computer, just insert the file in edit mode.
Michael Witbrock This tutorial was made for middle school students. I’m teaching in a different capacity now. Do you need files? What can I help you with?
@@Bigtigerfanmom Hi - don't need anything. It was useful. However, there is a point about 5:30 seconds in, where you load a file PhylogeneticTreeComparison.fas, which most of the 96K viewers of the video won't have -- I constructed a version of the file myself, after working out that it wasn't a standard demo file provided with MEGA. Perhaps you could add a link to a video where you show the watchers how to construct that file, by using the BI codes to find the other 5 genomes on NCBI. Fantastic that you're making this resource for intermediate school students, but maybe with a couple of tweaks it could be useful to even more people. All the best
@@MichaelWitbrock I think I have the file on an old Apple computer (back in the day when I could afford that type of computer). I'll check for it and post it in the notes after work today.
Thank you so much! My supervisor asked me to compile one for my thesis but totally left me hanging on how to do it. :) There is only one thing: Your alignment looked very good as you mention youself. What do you if you do see problems? I think I vaguely remember that you can crop positions at the end and beginning if they look too messy.
why did you put an accession number to find K. lactis from the database? is it a reference strain? Do we have to put reference strain when constructing a phylogenetic tree? Thanks
sebo oz Technology probably has changed since I made this tutorial. I have not worked with genetics actively for sometime now, as my role at work changed. You probably don’t have to have an accession any longer. I’m pretty sure, though, we did at the time.
Hi. So i had to go and get each homolog fasta for the HTT gene. But now when I export the alignment and head to do my phylogenetic tree, it won’t let me select what i just exported. Any suggestions?
It's got to be related to the type of file, in my opinion, that you're uploading. Please check the extension of the file and see if the software you're using accepts that.
Sir, I am aligning sequencing in MEGA format, but after opening the same file, I am getting message "Align Sequences must be of equal length". How to fix this problem?
@@Bigtigerfanmom Hi Lisa! I have the same issue that I can't find or probably don't have the Phylogenetic tree comparison file. What do you do when you say request permission to have the file from UW Madison? Thank you so much for posting this tutoial :) I hope I can finish making my tree soon.
Actually, I have not taught middle school in years. I think you should contact a local academic university for the most recent information. I am scared I won’t be the help you need.
Here's a Google Drive with some examples to explore:
drive.google.com/open?id=1N8EcmMmua6J3loMoEr5JBX7PhTSI29pf
Thanks so much Lisa.
Hi, may I ask why I click insert sequence from file, and I used the sample from the google drive (U94922 misson file), its not working.. it says the mega cant read the sequence
Do you get an error message? What does it say?
Even with a more recent version of MEGA this tutorial still worked perfectly! Thank you :)
Jesus Christ, finally someone with an understandable accent. Thanks.
This was soooo helpful for an assignment I was stuck in because MEGA kept rejecting the sequences I aligned on ClustalX!!!!!!!!!!!!!!!!!!!!! YOU ARE A LIFE-SAVER HONESTLY THANK YOU SO MUCH!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Thank you Lisa this video is easy to follow and all steps are clear.
Thanks Lisa!
Thanks ms. Lisa! It was very helpful!
Thank you very much Lisa :)
thank you so much! This was really helpful
Thank you!
I tried to do the same, but Mega opened it with txt file, not directly to allignment explorer? am i doing correct way as you did?
Good video. A few queries: what do the nos 0.001, 0.003 in the clades mean? How can I do bootstrapping? And how do I add the timescale?
Thank you so much madam. i was struggling a lot. but your video really helped me. i am your fan from India.
My pleasure, Kanaka!
Thank you Lisa.
Thank you Lisa.... very useful
Thanks, Lisa for the video! I found it!
Thanks a lot for sharing 😀
hank you so much! This was really helpful.
Thank you very much for your help :)
Thank you very much, it is well infomative lecture
ur the best....thank you..and yes i drink milk and read books...
Really helpful , many thanks Lisa! Can I ask about the percentage or numbers that can be added to the tree image and if I can add a unit to the scale?
Mushtaq Al-Esawy I’m really unsure of that threshold. I never “maxed out”, but my role has changed from science to library literacies.
very nice Dear Madam
I accept you as my teacher
Why my computer showed that error#4512 when kicking within group distance?
Thank you so much
Thank you so much this vídeo help me in my tesis
Thanks a lot for sharing :***
Of course, you or I will not have the pre-loaded phylogentic tree file with the 5 other kinds of Kluyveromyces partial ribosomal genes waiting to be added in "edit". And they are extremely hard to search for in NCBI. (the Accession numbers in the screenshot aren't very helpful. BUT the GI numbers like 31581082, 4038945 etc (at the left of the species ID in MEGA) are. So, tediously search for each of those, send it to a FASTA file, and insert each of those files into MEGA. Sigh. Also, the automated open in MEGA on download thing seems to be a Mac "feature" and super dangerous. If on another kind of computer, just insert the file in edit mode.
Michael Witbrock This tutorial was made for middle school students. I’m teaching in a different capacity now. Do you need files? What can I help you with?
@@Bigtigerfanmom Hi - don't need anything. It was useful. However, there is a point about 5:30 seconds in, where you load a file PhylogeneticTreeComparison.fas, which most of the 96K viewers of the video won't have -- I constructed a version of the file myself, after working out that it wasn't a standard demo file provided with MEGA. Perhaps you could add a link to a video where you show the watchers how to construct that file, by using the BI codes to find the other 5 genomes on NCBI.
Fantastic that you're making this resource for intermediate school students, but maybe with a couple of tweaks it could be useful to even more people. All the best
@@MichaelWitbrock I think I have the file on an old Apple computer (back in the day when I could afford that type of computer). I'll check for it and post it in the notes after work today.
@@Bigtigerfanmom That would be fantastic. I hope you found it!
Michael drive.google.com/drive/mobile/folders/1N8EcmMmua6J3loMoEr5JBX7PhTSI29pf?usp=drive_open
Thanks allot for this greatfull simply vedio , my question is how we can know the code of for example bacteria ? What's the step to do that?
Nice 👍
Thank you
Ma'am u have to mention about from where u have got the full file U94922, please help
thanks
Hello Ms. Lisa,where can I possibly start trimming my allignment from the start and end region.
You can tell where the pattern starts and ends. Trim the outliers off; usually that happened on both ends.
How we can know what is the accession number? And download sequence of bacteria and make three of alignment? And thank you
do we need to clean the sequences before running mega?
Yes, you'd want high-quality data to create the best results in MEGA.
Thank you so much! My supervisor asked me to compile one for my thesis but totally left me hanging on how to do it. :)
There is only one thing: Your alignment looked very good as you mention youself. What do you if you do see problems? I think I vaguely remember that you can crop positions at the end and beginning if they look too messy.
how do i download phylogenetic comparison file?
why did you put an accession number to find K. lactis from the database? is it a reference strain? Do we have to put reference strain when constructing a phylogenetic tree? Thanks
sebo oz Technology probably has changed since I made this tutorial. I have not worked with genetics actively for sometime now, as my role at work changed. You probably don’t have to have an accession any longer. I’m pretty sure, though, we did at the time.
@@Bigtigerfanmom thanks, so sequencing the data is enough I think. Without reference strain
hello, the video is really helpful but i am stuck at obtaining phylogenetic tree comparison files. how did you obtain yours
Morolake Ayeyo google drive is pinned
It's from University of WI - Madison (research university)
YES
Hi. So i had to go and get each homolog fasta for the HTT gene. But now when I export the alignment and head to do my phylogenetic tree, it won’t let me select what i just exported. Any suggestions?
It's got to be related to the type of file, in my opinion, that you're uploading. Please check the extension of the file and see if the software you're using accepts that.
Was the file cleaned up (cropped where it gets messy) before the export? Also, maybe the Bioinformatics-2 by JSBiology tutorial may help?!?
Also, go to 5:36 on my tutorial and rewatch the segment following that time. I wonder if that is the problem.
Tq Lisa for sharing
Thank you for this Video. Please, kindly send link to download MEGA on MAC
Try this: www.megasoftware.net/dload_mac_gui
Sir, I am aligning sequencing in MEGA format, but after opening the same file, I am getting message "Align Sequences must be of equal length". How to fix this problem?
Can you trim the ends? I’ve not seen that before. Otherwise, call a research university in your area- genetics research.
Hi, that was very informative and life made easy. Please assist, I does not give me the MEGA option (I do have the MEGA v7 software)
Magagula Nkululeko B I would have no idea. I would call your nearest research academic university.
From where can I get phylogenetic tree comparison file?? KIndly help
ranjan pandey Hello! It’s UW Madison’s file, but I will request permission for you to have it, too.
@@Bigtigerfanmom thank you ma'am. Your video was of great help. Yeah i have sorted out the issue i was facing.
How can we add bootstraping (values) in the phylogenetic tree??
@@Bigtigerfanmom HI Sorlie, I have the same problem, I cannot find phylogenetic tree comparison file in my laptop ? please help me
@@Bigtigerfanmom Hi Lisa! I have the same issue that I can't find or probably don't have the Phylogenetic tree comparison file. What do you do when you say request permission to have the file from UW Madison? Thank you so much for posting this tutoial :) I hope I can finish making my tree soon.
Hi, Thank you very much. Where I can get Mega program??
www.megasoftware.net/dload_win_gui
@@Bigtigerfanmom Realy Thank you
@@fixfalcon979 glad to help
Can we use the same tool for protein
Try it. I’m not sure.
@@Bigtigerfanmom thank you so much ☺️
thank you. But talking about organism information and choosing different options make the video unneccesary lengthy.
How can we contact with u maam
Laiba Fahad What do you need?
Actually, I have not taught middle school in years. I think you should contact a local academic university for the most recent information. I am scared I won’t be the help you need.
@@Bigtigerfanmom i am a research student and my task is to construct a phylogenetic tree and then i will ANI it
I think i will need your help
Drink milk !, read books ! hahahahahah