output visualization?

[melisaolave]

Hello,
just wondering what would be the most convenient way to visualize the output tree including the estimated divergence times expressed as branch lengths? is there any program that takes this output format? FigTree does not (I think)

Thanks!

Melisa

[MattSOlson]

This is also my question. Because of the complexity of the Newick format it is hard for me to see which times belong with which nodes, and I do not want to edit it by hand. When loaded into FigTree this output format did not generate an ultrametric tree with only the input taxa. I will also look into other programs, but a quick search suggests that the output Newick format may not be standard (I may be wrong about that as I am not familiar with the extended Newick formats). Any help to make the output more easily viewable would be appreciated. One idea might be to make a script to generate newick files with the following: the branch length in the estimated relative time and the mutation rate as a label on each branch.

Thank you

Matt

[smirarab]

Uyen, can we look into this?

[MattSOlson]

Thanks. I think I figured it out. User error. Matt

…

Sent from my iPhone On Jun 15, 2021, at 1:42 PM, Siavash Mirarab ***@***.***> wrote:  Uyen, can we look into this? — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fuym2%2FwLogDate%2Fissues%2F5%23issuecomment-861852664&data=04%7C01%7Cmatt.olson%40ttu.edu%7Cf84ad43ccf7b4b50742208d9304667f3%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C1%7C637593901221255852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=5XZQkyGcK5ysn6uWejruOZcPNPOZXKb9OVgurvBNbMU%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAHZBSYDND57C452VYA7I7UTTS7CKPANCNFSM4TBLTFMA&data=04%7C01%7Cmatt.olson%40ttu.edu%7Cf84ad43ccf7b4b50742208d9304667f3%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C1%7C637593901221255852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=3saNmRj0xvVfGzXeor9C%2FU%2BW%2FvZROKoDHl94LQ%2FGN%2Fk%3D&reserved=0>.

[smirarab]

Matt, Can you describe what the error was?

I am not able to open the output in FigTree still unless I remove the internal node labels. I am wondering how you managed to get around that.

For record, until we fix the issue, internal node labels can be removed using newick utilities:

nw_topology -Ib wlogdateoutput.tre > wlogdateoutput-nointral.tre

[MattSOlson]

Dear Mirarab, I cannot remember right now. I’m in the field for the next week. I will look into it when I return. Matt

…

Sent from my iPhone On Jun 15, 2021, at 2:33 PM, Siavash Mirarab ***@***.***> wrote:  Matt, Can you describe what the error was? I am not able to open the output in FigTree still unless I remove the internal node labels. I am wondering how you managed to get around that. For record, until we fix the issue, internal node labels can be removed using newick utilities: nw_topology -Ib wlogdateoutput.tre > wlogdateoutput-nointral.tre — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fuym2%2FwLogDate%2Fissues%2F5%23issuecomment-861878833&data=04%7C01%7Cmatt.olson%40ttu.edu%7Cd62aeffe93934962962f08d9304d9dcd%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C0%7C637593932182704673%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2FAhdXtxU56JZk8K1ChCr0agrxB3KNiayIPPpyv7aGwY%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAHZBSYFNA4XHAR7FNQYFKE3TS7IMBANCNFSM4TBLTFMA&data=04%7C01%7Cmatt.olson%40ttu.edu%7Cd62aeffe93934962962f08d9304d9dcd%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C0%7C637593932182704673%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wgIVklwgeNY8qwHS2NsT%2FY9HwKeL16unHHV4wNzHQVc%3D&reserved=0>.