PhyloNetworks users

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Welcome! this is the place for users to post questions, report bugs, and interact. To download the software, manual, tutorial, see the documentation. Questions and bug reports can also be reported by opening a GitHub issue here.

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Rowan Schley, Cécile Ané5

Jun 5

Combining phylonetworks/SNaQ runs

Wow! Thank you very much Cécile Best Rowan On Tuesday 4 June 2024 at 21:28:10 UTC+1 Cécile Ané wrote:

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Combining phylonetworks/SNaQ runs

Wow! Thank you very much Cécile Best Rowan On Tuesday 4 June 2024 at 21:28:10 UTC+1 Cécile Ané wrote:

Jun 5

Juan David Tovar Duran, Cécile Ané2

May 29

It takes too long indeed for 86 tips. Something like 25 tips is around the maximum that snaq can

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It takes too long indeed for 86 tips. Something like 25 tips is around the maximum that snaq can

May 29

vijayabhaskar badireddi, Cécile Ané2

May 26

tree in newick format with no names for taxa

No: the reading / parsing function in PhyloNetworks will not accept tips that don't have a label.

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tree in newick format with no names for taxa

No: the reading / parsing function in PhyloNetworks will not accept tips that don't have a label.

May 26

Xuan, Cécile Ané4

May 16

Cannot finish run in time

If you have access to a cluster, doing 30 runs or 3 runs should take about the same time... I don

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Cannot finish run in time

If you have access to a cluster, doing 30 runs or 3 runs should take about the same time... I don

May 16

May 2

Possibility of applying PhyloNetworks to mitochondrial data

Hello there, I hope you're doing well! I'm wondering if using PhyloNetworks for mitochondrial

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Possibility of applying PhyloNetworks to mitochondrial data

Hello there, I hope you're doing well! I'm wondering if using PhyloNetworks for mitochondrial

May 2

Andrea Berardi, Cécile Ané5

Apr 30

increasing from h=1 to h=2 does not add a second hybrid node?

Thank you again, Cecile! I can give this a try. On Monday, April 29, 2024 at 5:18:18 PM UTC-4 Cécile

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increasing from h=1 to h=2 does not add a second hybrid node?

Thank you again, Cecile! I can give this a try. On Monday, April 29, 2024 at 5:18:18 PM UTC-4 Cécile

Apr 30

mos, Cécile Ané2

Apr 29

readMultiTopology err

The files "net0.out" and "net2.out" do not have multiple topologies: they start

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readMultiTopology err

The files "net0.out" and "net2.out" do not have multiple topologies: they start

Apr 29

AT, Cécile Ané3

Apr 18

-loglik 0.0 doubts

I really appreciate your answer! I read this paragraph, but I was surprised by this sudden parameter

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-loglik 0.0 doubts

I really appreciate your answer! I read this paragraph, but I was surprised by this sudden parameter

Apr 18

Matheus Salles, Cécile Ané2

Apr 12

Issue on re-rooting trees and networks

I would not trust the estimated networks that cannot be rooted by your outgroup clade. These networks

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Issue on re-rooting trees and networks

I would not trust the estimated networks that cannot be rooted by your outgroup clade. These networks

Apr 12

Matheus Salles, … Cécile Ané4

Feb 10

Error on SNaQ - parallel edges

Your starting network is just fine. I was able to reproduce the error, and it seems to affect just

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Error on SNaQ - parallel edges

Your starting network is just fine. I was able to reproduce the error, and it seems to affect just

Feb 10

Ollie White, … Ваня Двояшов3

Feb 8

data requirements

Hi, I also have the quaddRAD seq data and reference genome. I used ref_map.pl script in stacks to get

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data requirements

Hi, I also have the quaddRAD seq data and reference genome. I used ref_map.pl script in stacks to get

Feb 8

Lindsey Worcester, Cécile Ané2

10/3/23

weights/proportion of genes

Hi Lindsey, In some cases, the inheritance weights are not identifiable. In these cases, SNaQ uses

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weights/proportion of genes

Hi Lindsey, In some cases, the inheritance weights are not identifiable. In these cases, SNaQ uses

10/3/23

Emily Watts-Whitehead

7/10/23

Hello, I am using SNaQ on simulated data, and I am occasionally encountering this error: optimization

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Hello, I am using SNaQ on simulated data, and I am occasionally encountering this error: optimization

7/10/23

Ash M, Cécile Ané2

7/7/23

Can you use Asteroid as a starting tree & Which network is recommended to use as starting trees

Sure, any good estimate of the species tree (or network) is good to use. For runs with higher number

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Can you use Asteroid as a starting tree & Which network is recommended to use as starting trees

Sure, any good estimate of the species tree (or network) is good to use. For runs with higher number

7/7/23

Matias Köhler, Cécile Ané2

6/4/23

gCF from IQ-TREE

Hi Matias, thanks for asking! The short answer is 'no'. There would be 2 issues: one

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gCF from IQ-TREE

Hi Matias, thanks for asking! The short answer is 'no'. There would be 2 issues: one

6/4/23

pietro antolini, Cécile Ané3

4/17/23

snaq! problem reading starting topology

Thanks! That was the problem, now it works smoothly Il giorno giovedì 13 aprile 2023 alle 15:43:41

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snaq! problem reading starting topology

Thanks! That was the problem, now it works smoothly Il giorno giovedì 13 aprile 2023 alle 15:43:41

4/17/23

Boka Li, Cécile Ané2

3/30/23

How to choose the best one among networks with different hmax values?

it's unclear I agree!

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How to choose the best one among networks with different hmax values?

it's unclear I agree!

3/30/23

3/15/23

Bootsnaq does not generate .out file

Hi everyone, I performed different SNaQ analyses based on different hmax values, and the most

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Bootsnaq does not generate .out file

Hi everyone, I performed different SNaQ analyses based on different hmax values, and the most

3/15/23

Sheila Rodríguez, Cécile Ané2

2/4/23

not enough memory Unresolved

Hi Sheila, PhyloNet (in java) and PhyloNetworks (in julia) are different programs. I cannot help with

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not enough memory Unresolved

Hi Sheila, PhyloNet (in java) and PhyloNetworks (in julia) are different programs. I cannot help with

2/4/23

Kevin I. Sánchez, Cécile Ané7

12/31/22

Problems with quarnetGoFtest

Dear Cécile Thanks for the help! Best El viernes, 23 de diciembre de 2022 a la(s) 16:39:36 UTC-3,

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Problems with quarnetGoFtest

Dear Cécile Thanks for the help! Best El viernes, 23 de diciembre de 2022 a la(s) 16:39:36 UTC-3,

12/31/22

mparks, … Cécile Ané7

12/15/22

SNaQ with large dataset

absolutely: there's function "deleteleaf!" to prune a taxon from a phylogeny (gene tree

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SNaQ with large dataset

absolutely: there's function "deleteleaf!" to prune a taxon from a phylogeny (gene tree

12/15/22

郭岑, … AT3

12/12/22

Warning: "the network obtained by putting the new hybrid in node -9 is not good, inCycle,gammaz,containRoot: Bool[true, true, false], we will skip it"

Hi Claudia and Cèline, I was trying to used SNaQ, but for hmax = 4 and 5, I get -loglik 0.0. (I

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Warning: "the network obtained by putting the new hybrid in node -9 is not good, inCycle,gammaz,containRoot: Bool[true, true, false], we will skip it"

Hi Claudia and Cèline, I was trying to used SNaQ, but for hmax = 4 and 5, I get -loglik 0.0. (I

12/12/22

AT, Cécile Ané3

12/11/22

Hi Cécile, Thank you so much for your advice. I will check it carefully. Best wishes, Alicia El jue,

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Hi Cécile, Thank you so much for your advice. I will check it carefully. Best wishes, Alicia El jue,

12/11/22

11/1/22

The toplogy of phylonet generated by PhyloNetworks discordant to the species tree generated by Astral.

Dear Cécile, I have encountered a problem that the toplogy of my phylonet generated by PhyloNetworks

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The toplogy of phylonet generated by PhyloNetworks discordant to the species tree generated by Astral.

Dear Cécile, I have encountered a problem that the toplogy of my phylonet generated by PhyloNetworks

11/1/22

10/26/22

The topology of phylonet generated by Phylonetwork diffenrent from real species tree.

Hi: After i got the phylonet by using Phylonetworks, discordance was find between it and real species

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The topology of phylonet generated by Phylonetwork diffenrent from real species tree.

Hi: After i got the phylonet by using Phylonetworks, discordance was find between it and real species

10/26/22

kmko...@gmail.com, Cécile Ané3

10/19/22

are branch lengths necessary?

Hi, Thanks a lot, I will generate an estimate of some sort. Best, KK On Wednesday, October 19, 2022

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are branch lengths necessary?

Hi, Thanks a lot, I will generate an estimate of some sort. Best, KK On Wednesday, October 19, 2022

10/19/22

Marek Šlenker, Cécile Ané3

10/3/22

error in "readTableCF()" - deleterows! not defined

Thank you so much for this report Marek! I fixed the issue in this pull request (#188). A new version

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error in "readTableCF()" - deleterows! not defined

Thank you so much for this report Marek! I fixed the issue in this pull request (#188). A new version

10/3/22

Jie Liu, Cécile Ané3

8/30/22

error in "Pkg.build("RCall")"

Dear Cécile, Thanks for reply. Best, JIe 在2022年8月29日星期一 UTC+8 22:02:38<Cécile Ané> 写道： This is

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error in "Pkg.build("RCall")"

Dear Cécile, Thanks for reply. Best, JIe 在2022年8月29日星期一 UTC+8 22:02:38<Cécile Ané> 写道： This is

8/30/22

pok doo, Cécile Ané5

8/28/22

error in rootatnode

Dear Cécile, Thanks so much for your help. I have solved the problem by taking your advise. Best. Jie

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error in rootatnode

Dear Cécile, Thanks so much for your help. I have solved the problem by taking your advise. Best. Jie

8/28/22

Yasuto ISHII, Cécile Ané4

7/17/22

quarnetGoFtest! Error

Dear Cecile, I ran the function with nsim = 1000 as recommended in the tutorial. The script is: res =

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quarnetGoFtest! Error

Dear Cecile, I ran the function with nsim = 1000 as recommended in the tutorial. The script is: res =

7/17/22

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