Hey Emmanuel,

how many basepairs long is your whole genome sequence?

-Ijad

Whole genome tree will not provide any detail information, it would be messy anyway. What you want to compare? Structure or functions? Or taxonomic similarity?

my genome is about 410 mb

Hi Emmanuel,

to draw a full genome based phylogenetic tree is not informative as do a phylogenomic comparison of single copy orthologs proteins of your species and the species you want to compare with. My advice is to perform an OrthoMCL analysis using the proteome of your strain and the proteome of the other genome you want to use. In such case your phylogenetic tree would be much more informative. You potentially can use the same approach based on specific genes you might want to compare, extracting them from all genomes in study.

To evaluate whole genome alignment in order to perform a phylogenetic tree, you can use mauve to do the alignment of all the genomes, then use software like Phylip, Mrbayes, RAxML or other phylogenetic tools in order to use the results of mauve to construct your phylogenetic tree.

Hope to be helpful,

Domenico

I agree with @abhishek kumar for the suitable tool for the analysis.

Moreover, I support @Domenico too. What is your purpose of analysis. I would strongly suggest you to define your objective, before you really perform calculations.

Moreover, if you just have a single genome, what purpose would the whole genome alignment and comparison serve ? You can do a blast analysis and based on top results evaluate the pre-results, if it was what you wanted to see?

Download the genomes do multiple sequecnce alignment available at ebi.ac.uk it uses CLULSTAL PROGRAME do MSA then go for phylogenetic tree construction

it produces the MSA with phylogenetic tree open the .phy file using JAL view software or tree viwever

Use mega software and analysis to construct phylogenetic tree

Both MEGA and CLUSTLW you can use for MSA and if you want to make it by pair wise alignment method then BLAST distance tree is most easiest way to do it.

For all those are suggesting various software like MEGA, Clustal etc. unfortunately neither they don't understand what was actually asked in the question + they don't understand the principle nor they understand/know how the software works!

Abhijeet Singh What would your suggestion be? I am curious to know.

Chrystine Yan

to know what?

Please know first the specific gene you are going to use. I don't think you can run multiple sequence alignment using software because that is too long to interpret.

Try mafft its perfect for big data

https://mafft.cbrc.jp/alignment/server/

Emmanuel Nnaemeka Nnadi what is the organism?

https://cge.cbs.dtu.dk/services/NDtree/

hello you can try this server

Emmanuel Nnaemeka Nnadi Thank you for addressing this q. I wonder if you have found the ideal software for such a task. I tried NDtree and Megax but I had difficulties using both software/server. Mainly when I tried to upload the WGS data.

Abhijeet Singh As I understood from your comment, all the previous suggestions are not ideal, so could you please recommend software for building the Maximum likelihood phylogenetic tree to compare the WGS of several bacterial strains?

Mohannad Mahmoud

The term "WGS data" is generally used for the raw data. And you can not used the raw data for any kind on analysis. You need to first process the data and make de novo or reference based assembly. As it is highly unlikely to get complete genome without contamination or missing genes, the final product would be an assembly rather than a complete genome.

The phylogenetic analysis is the step after you have produced the best genome assembly with your data. And there is not defined parameters to get best results. It would depend on your experience in using any specific tool and the quality of your data. It might take a while to get the optimally best assemblies from your data.

Further, the question what is your purpose of whole genome based tree? The choice of tool and algorithm would differ for different purpose. Although NDTree can use raw data for tree building, it is very specific tool for certain taxa and I would not recommend it if you are not targetting that specific taxa. However, as suggested in previous posts CVTree or OrthoMCL can be used. I also like Orthofinder.

But everything depends on your aim and purpose.

Mohannad Mahmoud . If you dealing with bacterial genomes then you can perform a pangenome analysis with roary. This will generate some trees for you.

You can also use dRep to calculate the average nucleotide identity and generate some dendograms.

Here is a video that might help: https://youtu.be/S_sRo_85jhs

Abhijeet Singh. Actually, I meant by WGS, the whole annotated genome (not raw data, or core genes). thank you for your clear explanation, I will try the tools you suggest.

Vincent Appiah Previously, I used Roary, on the Galaxy platform, to get the core gene alignment, and use it as a base to construct the tree using FASTTEREE, as recommended by other users. However, visualization of the tree failed several times.

Thank you for sharing this video, I will follow its steps.

Mohannad Mahmoud Roary works well with prokka generated gff files.

You can also share the error message here.

please use this website (https://tygs.dsmz.de./) to draw Phylogenetic tree using whole genome sequence , just put genome accession numbers and get your tree. if you have more than 20 genomes you can send email ( [email protected] ) for upgrade your genomes numbers.

Mohsin Ali thank you for sharing the website (https://tygs.dsmz.de./) . It really helped me when I was in need. I confirm that it is user friendly as I am not an expert in bioinformatics!!

Gahamanyi Noel Welcome dear

A phylogenetic tree can be constructed directly from a VCF file. The simple software VCF2PopTree reads a VCF file and builds a tree in few minutes. It also produces pairwise distance matrix from a VCF file, which can then be used as an input file for the popular software such as MEGA.

Software: https://github.com/sansubs/vcf2pop

Paper: VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. PeerJ, Vol.7, e8213; 2019