incomplete sequencences

[Marco Forgia]

Good morning everyone,

I have a question for all the IqTree experts about a problem that I'm facing during these days.

I'm building some phylogenetic trees using protein sequences coming from viruses, I started to use IqTree instead of MEGA because it tooks me a lot less for model selection and tree construction with the web server.

When I was using MEGA, I used to produce alignments that were submitted to build a tree with a function active that allows to use only the conserved sites excluding gaps and ambiguous sites during tree construction. 

The question is: do Iqtree adjust somehow sequnence lenght and gaps in the alignment? I saw that there is a gap/ambiguity extimation at the beginning of the model extimation, what happen if the sequence fail that step? 

I could of course export the alignment keeping only the conserved sites, but I'm curious to understand if the algorithm can handle these situations. Indeed this question come from the fact that when I figured that I was not exporting the alignment 

without taking away the gaps I already had some tree built this way, and actually the resulted tree seems to be closer to the one I tried to build with MEGA than the tree resulted from the Iqtree analysis with the alignment containing just conserved sites. 

Thank you for your help, I'm neither a native speaker or an expert in the field so sorry for mistakes or basic/stupid question.

Marco

[Minh Bui]

Hi Marco,

On 14 May 2019, at 4:23 pm, Marco Forgia <marco....@unito.it> wrote:

Good morning everyone,

I have a question for all the IqTree experts about a problem that I'm facing during these days.

I'm building some phylogenetic trees using protein sequences coming from viruses, I started to use IqTree instead of MEGA because it tooks me a lot less for model selection and tree construction with the web server.

When I was using MEGA, I used to produce alignments that were submitted to build a tree with a function active that allows to use only the conserved sites excluding gaps and ambiguous sites during tree construction. 

The question is: do Iqtree adjust somehow sequnence lenght and gaps in the alignment?

No! IQ-TREE takes the input alignment as it is.

I saw that there is a gap/ambiguity extimation at the beginning of the model extimation, what happen if the sequence fail that step? 

Nothing happens. IQ-TREE will continue the analysis. It serves mainly as a warning. Some users may find that useful.

I could of course export the alignment keeping only the conserved sites, but I'm curious to understand if the algorithm can handle these situations.

Yes, you can of course filter that in MEGA and then inputs to IQ-TREE.

Indeed this question come from the fact that when I figured that I was not exporting the alignment 

without taking away the gaps I already had some tree built this way, and actually the resulted tree seems to be closer to the one I tried to build with MEGA than the tree resulted from the Iqtree analysis with the alignment containing just conserved sites. 

Thank you for your help, I'm neither a native speaker or an expert in the field so sorry for mistakes or basic/stupid question.

No worries, it’s the purpose of the forum. 

Does that answer your questions?

Minh

Marco

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