JuliaPhylo users

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Welcome! This is the place for JuliaPhylo users to post questions, report bugs, and interact.

The list of packages in the JuliaPhylo ecosystem is listed here: https://juliaphylo.github.io/JuliaPhyloWebsite/

Questions and bug reports can also be reported by opening a GitHub issues in the appropriate package repository.

0 selected

Wyclif Odago, … Cécile Ané7

Jun 17

ERROR: UndefVarError: `writeTableCF` not defined in `Main`

Try this in package mode (type ] to switch to package mode), to update to the most recent package

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ERROR: UndefVarError: `writeTableCF` not defined in `Main`

Try this in package mode (type ] to switch to package mode), to update to the most recent package

Jun 17

Brock Wooldridge, Cécile Ané3

May 8

Help with interpretation of SNaQ output network

Hi Cécile, Thank you so much for the explanation and the sketches. In particular, thinking of them as

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Help with interpretation of SNaQ output network

Hi Cécile, Thank you so much for the explanation and the sketches. In particular, thinking of them as

May 8

Érico Polo, Cécile Ané3

Jan 4

How low-supported nodes in gene trees affect SNaQ?

Hello, thank you very much for your prompt reply! I remember that when I first started experimenting

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How low-supported nodes in gene trees affect SNaQ?

Hello, thank you very much for your prompt reply! I remember that when I first started experimenting

Jan 4

Colin Beckingham

12/26/24

Python versus Julia distance counts

The website rosalind.info offers a puzzle where we are given a set of networks in very loose Newick

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Python versus Julia distance counts

The website rosalind.info offers a puzzle where we are given a set of networks in very loose Newick

12/26/24

Marek Šlenker

11/5/24

How to find the best network? sequential or parallel runs?

Hi there. Is there any difference in the chance to find the best network, when running snaq for 4

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How to find the best network? sequential or parallel runs?

Hi there. Is there any difference in the chance to find the best network, when running snaq for 4

11/5/24

Nick englewrye

10/9/24

How to deal with running out of memory during bootstrapping?

Hello everyone, I am currently having issues with running out of memory while trying to bootstrap. I

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How to deal with running out of memory during bootstrapping?

Hello everyone, I am currently having issues with running out of memory while trying to bootstrap. I

10/9/24

*, Cécile Ané2

9/6/24

Multiple alleles for bootnaq possible?

Short answer: bootsnaq with multiple alleles has not been implemented in a "one-does-it-all

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Multiple alleles for bootnaq possible?

Short answer: bootsnaq with multiple alleles has not been implemented in a "one-does-it-all

9/6/24

*, Cécile Ané2

9/6/24

Starting_tree

It should be a tree (or a network with as many reticulations or fewer, compared to the number of

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Starting_tree

It should be a tree (or a network with as many reticulations or fewer, compared to the number of

9/6/24

8/28/24

Bootstrap

Hi, I want to ask if it is possible to perform a bootstrap analysis directly on a phylogenetic

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Bootstrap

Hi, I want to ask if it is possible to perform a bootstrap analysis directly on a phylogenetic

8/28/24

Nick englewrye

8/12/24

Does anyone have a copy of Quartet MaxCut for download? The link seems to be down for about a week now.

Hello everyone, I was wondering if someone had a good mirror or some way to get Quartet MaxCut other

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Does anyone have a copy of Quartet MaxCut for download? The link seems to be down for about a week now.

Hello everyone, I was wondering if someone had a good mirror or some way to get Quartet MaxCut other

8/12/24

Rowan Schley, Cécile Ané5

6/5/24

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:

6/5/24

Juan David Tovar Duran, Cécile Ané2

5/29/24

Takes too long

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

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Takes too long

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

5/29/24

vijayabhaskar badireddi, Cécile Ané2

5/26/24

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.

5/26/24

Xuan, Cécile Ané4

5/16/24

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

5/16/24

Matheus Salles

5/2/24

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

5/2/24

Andrea Berardi, Cécile Ané5

4/30/24

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

4/30/24

mos, Cécile Ané2

4/29/24

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

4/29/24

AT, Cécile Ané3

4/18/24

-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

4/18/24

Matheus Salles, Cécile Ané2

4/12/24

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

4/12/24

Matheus Salles, … Cécile Ané4

2/10/24

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

2/10/24

Ollie White, … Ваня Двояшов3

2/8/24

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

2/8/24

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

SNaQ Error

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

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SNaQ Error

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

Ana VF

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