Groups

hahnlab-cafe

Contact owners and managers

1–30 of 267

Welcome to CAFE, software for Computational Analysis of gene Family Evolution.

The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.

0 selected

Paschalis Natsidis, … kavita kumari16

Sep 4

caferror fails to converge or initialise

hey could you solve the problem? If yes can u share what possible steps you have taken. thankyou. On

unread,

caferror fails to converge or initialise

hey could you solve the problem? If yes can u share what possible steps you have taken. thankyou. On

Sep 4

creo...@naver.com, … kavita kumari5

Aug 22

Failed to initialize any reasonable values

hello everyone, i am trying to running cafe on 63 species and it always throw the same error fail to

unread,

Failed to initialize any reasonable values

hello everyone, i am trying to running cafe on 63 species and it always throw the same error fail to

Aug 22

kavita kumari, Hahn, Matthew2

Aug 20

failed to initialise any reasonable values

Hello, I think it's that your branch lengths are much too short. You can either drop the very

unread,

failed to initialise any reasonable values

Hello, I think it's that your branch lengths are much too short. You can either drop the very

Aug 20

Meeran Hussain, Hahn, Matthew5

Jun 13

Clarification on family vs branch-level significance in CAFE5 outputs

Oh ok, thanks Hahn 🙂 On Fri, 13 Jun 2025 at 12:16 PM, Hahn, Matthew <m...@iu.edu> wrote: Hi

unread,

Clarification on family vs branch-level significance in CAFE5 outputs

Oh ok, thanks Hahn 🙂 On Fri, 13 Jun 2025 at 12:16 PM, Hahn, Matthew <m...@iu.edu> wrote: Hi

Jun 13

Daisy Sotero, … Ben Fulton6

Apr 18

Failed to initialize any reasonable values

Hi, This could also indicate an issue with your tree. We generally assume that a branch of length of

unread,

Failed to initialize any reasonable values

Hi, This could also indicate an issue with your tree. We generally assume that a branch of length of

Apr 18

F U, Hahn, Matthew5

Apr 7

comparing multiple two-lambda models

Yes, exactly right (though I wouldn't exclude the outliers). Your data definitely support the 2-

unread,

comparing multiple two-lambda models

Yes, exactly right (though I wouldn't exclude the outliers). Your data definitely support the 2-

Apr 7

P M, Hahn, Matthew2

Feb 22

sweet spot for speices or evolutionary time

Hi, It's a bit hard to follow everything here, but in general there is no optimal way to find k.

unread,

sweet spot for speices or evolutionary time

Hi, It's a bit hard to follow everything here, but in general there is no optimal way to find k.

Feb 22

张宁, … Hahn, Matthew7

Jan 23

cafe5 how to choose an proper k?

Yes, that is what I would recommend. You might try downsizing your dataset to a more closely related

unread,

cafe5 how to choose an proper k?

Yes, that is what I would recommend. You might try downsizing your dataset to a more closely related

Jan 23

Tingyu Shi, Hahn, Matthew2

10/11/24

Issue with CAFE Analysis about "Failed to initialize any reasonable values."

Hi, Did you try removing the top few families? That should be more effective. This is a very deep

unread,

Issue with CAFE Analysis about "Failed to initialize any reasonable values."

Hi, Did you try removing the top few families? That should be more effective. This is a very deep

10/11/24

Carmen Gibbs, Hahn, Matthew6

10/7/24

clarification on *-clade_results.txt

Ok thanks! On Monday, October 7, 2024 at 9:52:49 AM UTC-6 m...@indiana.edu wrote: Yes, exactly. If a

unread,

clarification on *-clade_results.txt

Ok thanks! On Monday, October 7, 2024 at 9:52:49 AM UTC-6 m...@indiana.edu wrote: Yes, exactly. If a

10/7/24

4/21/24

Base_report.cafe file

I am trying to run CAFE 5/1.1.0 and the Base_report.cafe file appears truncated (ie missing columns

unread,

Base_report.cafe file

I am trying to run CAFE 5/1.1.0 and the Base_report.cafe file appears truncated (ie missing columns

4/21/24

Rosa Celia Poquita-Du, Hahn, Matthew4

4/5/24

need help with interpreting CAFE5 output

Hi Ross, I guess I'm not sure what you're asking for. CAFE does give a branch by branch

unread,

need help with interpreting CAFE5 output

Hi Ross, I guess I'm not sure what you're asking for. CAFE does give a branch by branch

4/5/24

Jonathan Velotta, Hahn, Matthew5

3/20/24

CAFE5 rapidly evolving genes

Wonderful. And thanks for creating the tool! On Wed, Mar 20, 2024 at 10:56 AM Hahn, Matthew <mwh@

unread,

CAFE5 rapidly evolving genes

Wonderful. And thanks for creating the tool! On Wed, Mar 20, 2024 at 10:56 AM Hahn, Matthew <mwh@

3/20/24

Andreas Wallberg, Hahn, Matthew2

3/17/24

Correction for multiple testing?

Hi Andreas, I would say you definitely have to correct for multiple tests. The size of the family

unread,

Correction for multiple testing?

Hi Andreas, I would say you definitely have to correct for multiple tests. The size of the family

3/17/24

11/27/23

Recent spam messages

We've had minimal disruption of the CAFE group in the several years it's been in existence. I

unread,

Recent spam messages

We've had minimal disruption of the CAFE group in the several years it's been in existence. I

11/27/23

11/7/23

Scripts for parsing CAFE5 output?

Hello, I'm currently using CAFE5 for the first time, and I'm having a bit of trouble parsing

unread,

Scripts for parsing CAFE5 output?

Hello, I'm currently using CAFE5 for the first time, and I'm having a bit of trouble parsing

11/7/23

Hahn, Matthew, … Upuli Nakandala4

10/22/23

Hi Upuli, Thanks so much for your work including CAFE in Orthovenn. It is much appreciated. As for

unread,

Hi Upuli, Thanks so much for your work including CAFE in Orthovenn. It is much appreciated. As for

10/22/23

VT, Hahn, Matthew2

9/7/23

Comparing models through simulations

1000 would be my recommendation, but 100 is likely fine. cheers, matt On Sep 7, 2023, at 11:59 AM, VT

unread,

Comparing models through simulations

1000 would be my recommendation, but 100 is likely fine. cheers, matt On Sep 7, 2023, at 11:59 AM, VT

9/7/23

Alexandre Fernandes, Hahn, Matthew4

9/5/23

"Failed to initialize any reasonable values" on small dataset

I think the tree is too long. Sorry! On Sep 5, 2023, at 6:33 PM, Alexandre Fernandes <

unread,

"Failed to initialize any reasonable values" on small dataset

I think the tree is too long. Sorry! On Sep 5, 2023, at 6:33 PM, Alexandre Fernandes <

9/5/23

Anezka Santolikova, Hahn, Matthew2

7/26/23

Compare models in cafe5

Hi Anezka, The problem is that the distribution of log-likelihoods may not be chi-squared distributed

unread,

Compare models in cafe5

Hi Anezka, The problem is that the distribution of log-likelihoods may not be chi-squared distributed

7/26/23

Sebastian Lee, … Ben Fulton7

7/21/23

CAFE5 'inf' issue with small tree

I think this is a bug in CAFE in handling family sizes > 1000. You don't actually have any

unread,

CAFE5 'inf' issue with small tree

I think this is a bug in CAFE in handling family sizes > 1000. You don't actually have any

7/21/23

Subhajeet Dutta, … Dr. Suresh Kumar3

7/14/23

Installation problem with r8s

Hi, i was also facing issues in r8s installation . so i tried alternate way to convert your tree to

unread,

Installation problem with r8s

Hi, i was also facing issues in r8s installation . so i tried alternate way to convert your tree to

7/14/23

Wenqiang Shi, … Ben Fulton10

7/10/23

Comparing two lambda models and error in simulation in cafe5

Thanks for the response. I will have a try. Best regards, Wenqiang On Sat, Jul 1, 2023 at 3:30 AM Ben

unread,

Comparing two lambda models and error in simulation in cafe5

Thanks for the response. I will have a try. Best regards, Wenqiang On Sat, Jul 1, 2023 at 3:30 AM Ben

7/10/23

Lin Rikka, Ben Fulton2

6/27/23

Families with largest size differentials

Do you mean, it continued to fail to find values? You will have to remove more families.

unread,

Families with largest size differentials

Do you mean, it continued to fail to find values? You will have to remove more families.

6/27/23

Faheema Kalsoom Khan

5/3/23

Is there any limit on the minimum number of gene families to use in CAFE analysis?

Hi, I am a PhD student at Uppsala University of Sweden. I have been trying to run CAFE with very few

unread,

Is there any limit on the minimum number of gene families to use in CAFE analysis?

Hi, I am a PhD student at Uppsala University of Sweden. I have been trying to run CAFE with very few

5/3/23

biotek...@gmail.com, Hahn, Matthew4

4/25/23

Families with largest size differentials:

Hi, The tree is still not ultrametric. Also, can you tell me approximately how deep the tree is in

unread,

Families with largest size differentials:

Hi, The tree is still not ultrametric. Also, can you tell me approximately how deep the tree is in

4/25/23

Elisa Ramos, … biotek...@gmail.com3

4/25/23

families with the largest difference

Hi All, Im having the same issue , wondering how did you fix the issue, what steps are good to tacke

unread,

families with the largest difference

Hi All, Im having the same issue , wondering how did you fix the issue, what steps are good to tacke

4/25/23

Francesco Cicconardi, Hahn, Matthew4

4/20/23

Checking convergence

Pretty close, yeah. On Apr 20, 2023, at 5:58 AM, Francesco Cicconardi <fran...@gmail.com>

unread,

Checking convergence

Pretty close, yeah. On Apr 20, 2023, at 5:58 AM, Francesco Cicconardi <fran...@gmail.com>

4/20/23

Filippo Nicolini, Hahn, Matthew4

4/19/23

Likelihood ratio distributions not converging

Yes, re-running some of these should help. It's good that the distribution with two lambdas

unread,

Likelihood ratio distributions not converging

Yes, re-running some of these should help. It's good that the distribution with two lambdas

4/19/23

Rijan Dhakal, Hahn, Matthew2

3/29/23

Trying to understand the pharasing in the documentation.

Hi Rijan, Thanks for your question—this is a common confusion about likelihoods (not just in CAFE).

unread,

Trying to understand the pharasing in the documentation.

Hi Rijan, Thanks for your question—this is a common confusion about likelihoods (not just in CAFE).

3/29/23

Search

Clear search

Close search

Google apps

Main menu