phylogenetic tree of 66 genes common in several cp genomes

Question

[avnim]

How to create phylogenetic tree of 66 genes shared by all 30 chloroplast genomes? I fetched the sequences of genes in particular order for all the cp genomes then tried to create using mega but didn,t worked out. Please help. Thanks in advance.

[GenoMax]

tried to create using mega but didn,t worked out

Without giving details about what did not you work it would be difficult to get help with this. Have you checked out MEGA tutorials? You would want to build individual trees for the 66 genes. Not sure if you tried doing it that way.

[avnim]

No, I didn,t want to build individual trees, I have to make one tree out of 66 genes common in all 30 cp genomes. It is taking too long to align in mega so tried using clustal. the issue remains the same so did with mafft then build using mega but the resulted output was inappropriate.

[avnim]

Hello avantika.maurya!

got the answer for my query :)

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Joe]

There is no need to close threads once they're answered, just accept the relevant answers.

Answer 1

[flogin]

You must follow these steps:

• Align your sequences: you can easily do this with MAFFT online.
• Edit your alignment: you can do this with Gblocks.
• Evaluate the best substitution model
• Run your phylogeny.

You must be very careful in each step, have several methods of alignments with different strategies, you can read the help of MAFFT to set correctly each parameter.

Gblocks by default is extremely strict if your alignment has several non-conserved positions the Gblocks will remove then, you can "flexibilize" the Gblocks edition, changing the block parameters.

The substitution model can be evaluated by Jmodel (for nucleotides) or ProtTest (for amino acids), or you can use the SMS tool in the ATCGPhyML platform (online).

At least, read about the different phylogeny methods (UPGMA, Maximum Parsimony, Maximum Likelihood and Bayesian), think which method is the best for your analysis, and how you can perform your phylogeny in the right manner.

If you use a Bayesian approach, you can use Mr.Bayes or BEAST. If you use a Maximum Likelihood approach, you can use the PhyML (present in the online version or SeaView platform for Linux) or the RaxML tool (it's a good choice if you are working with genes from polyprotein, because you can set different substitutions model by region of your sequence).

links:

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

http://www.atgc-montpellier.fr/phyml/

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

I hope that it can help u.

Best,

[avnim]

Thanks, it was helpful. I already aligned using standalone mafft since the file size exceeds the limit of input file for online server, then tried to build the tree using mega and also with paup but got inappropriate results. Gblocks may be a help to this and then evaluating the model. Thank you again

Answer 2

[Joe]

A couple of options:

Cluster all the orthologues from each genome and perform multiple sequence alignments for each.

Then:

• concatenate the alignments, and create a tree from this concatenated alignment with an algorithm of choice.

Or

• compute gene trees for each gene cluster, and then create a consensus tree with a tool like ASTRAL.

———

Alternatively, depending on what your end goal is, it may be sufficient to compute ANI, or mash sketch based trees from the whole genomes.

[avnim]

Thank you very much. This is very useful suggestion.