Bins all of size 1

[BenjaminBlanchard]

Hello! Step 1 and Step 2 complete fine for me, but when Step 3 completes, it produces 1,300 bins (i.e. one bin for each one of my 1,300 genes). The command I entered was:

python $BINNING_HOME/cluster_genetrees.py genes 50

Do you have any guidance one why this might be happening?

[smirarab]

Did the genes have support values between 0 and 100?

On Thu, Nov 7, 2019 at 2:13 PM BenjaminBlanchard notifications@github.com wrote:

Hello! Step 1 and Step 2 complete fine for me, but when Step 3 completes, it produces 1,300 bins (i.e. one bin for each one of my 1,300 genes). The command I entered was:

python $BINNING_HOME/cluster_genetrees.py genes 50

Do you have any guidance one why this might be happening?

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-- Siavash Mirarab

[BenjaminBlanchard]

Thanks for the reply! Do you mean in the pairwise output files (e.g. "uce-997.50")? If so, these values are between 0 and 100, yes (e.g. "uce-997 uce-682 51 82" or "uce-997 uce-721 41 30"). Or did you mean the gene trees, or something else?

[BenjaminBlanchard]

(If you meant gene trees, these also have support values between 0 and 100)

Here's an example of my gene tree, .fasta file, and .50 file output from Step 2, attached (added .txt to each file so I could attach it here). iqtree_bootstrap.treefile.txt uce-997.50.txt uce-997.fasta.txt

And here is my commands.compat.50 file from Step 1, too, in case that is amiss somehow (added .txt for upload here as well).

commands.compat.50.txt

[smirarab]

Meant gene trees. My guess is that you do have highly supported conflicts. For results change if you try 75 or 90 as threshold?

On Fri, Nov 8, 2019 at 6:15 AM BenjaminBlanchard notifications@github.com wrote:

(If you meant gene trees, these also have support values between 0 and 100)

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[BenjaminBlanchard]

Thanks again for the reply: I just tried a threshold of 75 and it still produced 1,300 bins of size 1... I'll try 90 next.

[BenjaminBlanchard]

Well... with a threshold of 90, it output 1,270 bins, ha. So technically not 1,300, but does this mean that for some reason binning will not be useful for my data?

[smirarab]

Yes, Benjamin. It seems binning is not useful here as gene trees do seem to have highly supported conflicts. You can simply report that on this dataset, binning refuses to bin genes together due to the presence of highly supported conflicts.

On Mon, Nov 11, 2019 at 11:08 AM BenjaminBlanchard notifications@github.com wrote:

Well... with a threshold of 90, it output 1,270 bins, ha. So technically not 1,300, but does this mean that for some reason binning will not be useful for my data?

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[BenjaminBlanchard]

Alright - thank you so much for your help!!!