orthovenn3

[Hahn, Matthew]

Just forwarding this to the list.

Begin forwarded message:

From: Subhajeet Dutta <subhaj...@gmail.com>

Subject: Re: Installation problem with r8s

Date: May 2, 2023 at 1:08:04 PM EDT

To: "Hahn, Matthew" <m...@indiana.edu>

Hello, 

         Recently orthovenn3 has released where cafe5 is integrated and we can do gene family expansion and contraction analysis there. I have run for my genomes and get the result where different files are generated. Such as following :

In base clade result, #Taxon_ID Increase Decrease is given but that does not match with the number mention in the tree.

Secondly how do i know which clusters are expanded or contracted in any particular organism?

Can you help me regarding this?

[Ben Fulton]

Base clade result doesn't show the number of unchanged families, so you can find that number by subtracting the increase and decrease counts from the total number.

The Base_change.tab file is a table showing the increases and decreases for each node of the tree, for each species.

Does that answer your question?

--

Ben Fulton

Indiana University

On Tuesday, May 2, 2023 at 2:06:28 PM UTC-4 Matthew Hahn wrote:

Just forwarding this to the list.

Begin forwarded message:

From: Subhajeet Dutta

Subject: Re: Installation problem with r8s

Date: May 2, 2023 at 1:08:04 PM EDT

To: "Hahn, Matthew" 

[Upuli Nakandala]

Hi Ben,

I also did cafe5 integrated in Orthovenn3. It has generated a phylogenetic tree on which the expanded and contracted gene families are indicated on pie charts for each species. We can click on these numbers and download the protein sequences that were expanded and contracted for each species. 

But when I open that file (expanded/contracted genes for one species), I found that the file contains a list of protein sequences derived from all the species that I included in the analysis. 

My question is whether that is correct or not. I was expecting to have expanded or contracted genes for that particular species in the final result file. Since I have not done the Cafe using command line, I need to know whether we get the same type of results in Cafe5 when we do it using command line option.

I need to explore the functions of the expanded and contracted gene families in each species. I thought of getting the gene IDs for expanded/contracted gene families from each separately and subject to functional annotation. But I am not sure how I should do that since the results file contains the protein sequences for all the species. 

Thanks and regards,

Upuli

[Hahn, Matthew]

Hi Upuli,

Thanks so much for your work including CAFE in Orthovenn. It is much appreciated.

As for your question, CAFE does not identify which genes in a family have expanded or contracted, only the number that have been gained or lost in that family. So while you could get the list of families with expansions or contractions on a branch, it is not possible to get a list of genes.

cheers,

Matt 

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