How to make circular heatmap / how to make newick tree / heat map with phylogenetic tree / TBTool

In this video we will expressed our expression data or any other data through circular heatmap. For constructing heatmap, we need our genes expression data or any other data in figure form, and protein sequence of that genes. First we construct the newick tree in MEGA and then use that newick tree and expression data in TBTool to construct the circular heatmap with phylogenetic tree.
#heatmap
#phylogenetictree
#genomewidestudy
#TBTool
#mega

[@MamtaSingh-gp9tz]

Your videos are awsome

[@genomewidestudy]

Thanks

[@Gbemi78]

Insightful videos as always

[@genomewidestudy]

Much appreciated

[@WickyReacts]

quite helpful. Thank you

[@WickyReacts]

Can i draw the circle figure without including the phylogenetic tree?

[@genomewidestudy]

Yes, you can

[@genomewidestudy]

Use same option without newick tree.. You will get the circular figure without tree.

[@enjoycutness]

Awesome

[@genomewidestudy]

Thanks.for comment

[@enjoycutness]

@@genomewidestudy where are you from?

[@castilloh.gianmarco1048]

Good classe
Salute Perú.

[@genomewidestudy]

Thanks

[@castilloh.gianmarco1048]

@@genomewidestudy Excuse me for commenting so much, but can you help me with TBtools.
I get a black screen with error.

[@MrRamaeri]

Hello Sir, thank you so much for you video. Very nice . I followed this, I am not getting tree using Newick value. Could help me?

[@genomewidestudy]

May be something wrong with your newick tree..in copy past or other. Retry

[@evlampiaparcharidou9882]

Hey! Very useful video, thanks a lot! Which type of data do you use as input? What is the data in your excel file? Raw counts or normalised, as for example TMM.?
And the way you did the heatmap, is the log2 normalisation used, right? Not z-score.?

[@genomewidestudy]

thanks for comment

[@genomewidestudy]

its only a example. you can use any nomaricall data to make the heat map. you can use expressiin data, mean data of you parameters, depends on your analysis

[@evlampiaparcharidou9882]

@@genomewidestudy Thanks a lot!

[@MamtaSingh-gp9tz]

Hello sir, please let know how we can find gene location on chromosome if only scaffolds information available for a gene in phytozome. I have some sequences which contain only scaffold information.

[@genomewidestudy]

Then use that scaffold in place of chromosome

[@MamtaSingh-gp9tz]

@@genomewidestudy ok sir. Thanks for reply

[@jennyshah2290]

Very helpful and can you tell me how to get tbtool

[@genomewidestudy]

it is free sofiware and you can easily download it from any search engin.

[@genomewidestudy]

Video about downloading and installing tbtool has been uploaded. You can get the guidance. Thanks

[@NasirHamad]

assalamualaikum sir I have 553 sequences of a virus in fasta file .....how can I make the input for this analysis.....

[@genomewidestudy]

walaikumusalam.
Use the same method and try

[@NasirHamad]

@@genomewidestudy ur right sir but I don't have the excel file like that .....I have fasta sequences.....how can I make that values

[@genomewidestudy]

what you want to do exactly.
You want to make Phylogenetic tree or want to make the heatmap of your expression data...

[@NasirHamad]

@@genomewidestudy sir I have orf sequences in fasta file downloaded from ncbi ...I don't have expression data ....how can I do such analysis with this file ???

[@genomewidestudy]

watch this video
czcams.com/video/pjXmI-j060A/video.html