PhyloPhlAn-users

Contact owners and managers

1–30 of 62

Welcome!

This group is meant to serve as a mailing list for notifying PhyloPhlAn users about new features, software updates, and for any questions or comments you may have.

PhyloPhlAn is descibed at:

https://bitbucket.org/nsegata/phylophlan

and the code is hosted by bitbucket:

https://bitbucket.org/nsegata/phylophlan/src

Nicola Segata

0 selected

4/22/20

PhyloPhlAn 3.0 release and closure of PhyloPhlAn Google Group

Hello everyone, The PhyloPhlAn repository has been migrated to GitHub due to the discontinued support

unread,

PhyloPhlAn 3.0 release and closure of PhyloPhlAn Google Group

Hello everyone, The PhyloPhlAn repository has been migrated to GitHub due to the discontinued support

4/22/20

Jie Liu, Francesco Asnicar6

4/9/20

No Access to Bitbucket

Hi Jie, With the conda installation it is a bit more tricky to comment that line. You can try that by

unread,

No Access to Bitbucket

Hi Jie, With the conda installation it is a bit more tricky to comment that line. You can try that by

4/9/20

hilbert.h...@gmail.com, … Konstantina Mitsi4

2/17/20

File "./phylophlan.py", line 393 except OSError, e:^ SyntaxError: invalid syn

So! Hello again! Problem solved! pyenv is not compatible with the ppa2 conda environment but it makes

unread,

File "./phylophlan.py", line 393 except OSError, e:^ SyntaxError: invalid syn

So! Hello again! Problem solved! pyenv is not compatible with the ppa2 conda environment but it makes

2/17/20

梅然, … Jagadeeshwari Uppada3

11/4/19

Running example error: ValueError: max() arg is an empty sequence

Hi even am facing the same issue "traceback (most recent call last):File "./taxcuration/

unread,

Running example error: ValueError: max() arg is an empty sequence

Hi even am facing the same issue "traceback (most recent call last):File "./taxcuration/

11/4/19

Yancong Zhang, Francesco Asnicar5

4/23/19

Issue with muscle error

Hi Francesco, Yes, I installed MUSCLE v3.8.31 and MAFFT v7.427. I tested them separately and both of

unread,

Issue with muscle error

Hi Francesco, Yes, I installed MUSCLE v3.8.31 and MAFFT v7.427. I tested them separately and both of

4/23/19

bkr...@ucdavis.edu, … Francesco Asnicar8

3/20/19

The dreaded assert vv not in prots2ups assertion error...

Hello Caroline, Can you provide the full command line and the version of PhyloPhlAn you're using?

unread,

The dreaded assert vv not in prots2ups assertion error...

Hello Caroline, Can you provide the full command line and the version of PhyloPhlAn you're using?

3/20/19

2/14/19

Too crazy about phylophlan!! Can anyone help me? Crying for~~

Hi, I have spent almost 8 hours in the installation of phylophlan, both version 1 and version 2. I am

unread,

Too crazy about phylophlan!! Can anyone help me? Crying for~~

Hi, I have spent almost 8 hours in the installation of phylophlan, both version 1 and version 2. I am

2/14/19

Jiffin Paulose, … Francesco Asnicar6

2/6/19

phylophlan.fna is empty

Dear Kevin, No problem, many thanks for checking the changelog in diamond. I'll add a check about

unread,

phylophlan.fna is empty

Dear Kevin, No problem, many thanks for checking the changelog in diamond. I'll add a check about

2/6/19

1/17/19

Marker genes and missin/over-represented genes

I have some questions I could not find an answer to in regards to how PhyloPhlAn operates. I was

unread,

Marker genes and missin/over-represented genes

I have some questions I could not find an answer to in regards to how PhyloPhlAn operates. I was

1/17/19

Soo-Je Park, Francesco Asnicar3

12/5/18

hg clone https://bitbucket.org/nsegata/phylophlan - SSL error

Thanks. Francesco, I will try to fix that. But, on 12.04 lts, the command is working. however, the

unread,

hg clone https://bitbucket.org/nsegata/phylophlan - SSL error

Thanks. Francesco, I will try to fix that. But, on 12.04 lts, the command is working. however, the

12/5/18

Nicola Segata, … SJ Park3

12/5/18

Re: Phylophlan error

good!!!! Malte. thanks. your reply, finally, seriously helpful to me. thanks!!!!! 2015년 10월 5일 월요일 오후

unread,

Re: Phylophlan error

good!!!! Malte. thanks. your reply, finally, seriously helpful to me. thanks!!!!! 2015년 10월 5일 월요일 오후

12/5/18

Jiffin Paulose, Francesco Asnicar2

11/9/18

Error at "gene_tree2" step

Many thanks for reporting this. I actually tried (a while back) the gene tree pipeline and never

unread,

Error at "gene_tree2" step

Many thanks for reporting this. I actually tried (a while back) the gene tree pipeline and never

11/9/18

Jiffin Paulose, Francesco Asnicar7

11/3/18

error during Mapping "phylophlan"

Francesco, it appears to be working! I'm running through a dataset right now, I'll keep you

unread,

error during Mapping "phylophlan"

Francesco, it appears to be working! I'm running through a dataset right now, I'll keep you

11/3/18

Jiffin Paulose, Francesco Asnicar11

11/2/18

FastTree not found, installed and in PATH

I see, indeed then it is the way the environment is handled by the node. Alternatively, you can

unread,

FastTree not found, installed and in PATH

I see, indeed then it is the way the environment is handled by the node. Alternatively, you can

11/2/18

hza...@gmail.com, Francesco Asnicar3

10/26/18

Error when use myself database

Thanks. It works when i use input folder. Huifeng Francesco Asnicar <francesc...@gmail.com

unread,

Error when use myself database

Thanks. It works when i use input folder. Huifeng Francesco Asnicar <francesc...@gmail.com

10/26/18

Ilia Burgsdorf, Francesco Asnicar2

10/3/18

Bootstrap support for the final RAxML_bestTree.project_name_refined.tre

Dear Ilia, Thanks for using PhyloPhlAn. Be careful that the FastTree support values are not "

unread,

Bootstrap support for the final RAxML_bestTree.project_name_refined.tre

Dear Ilia, Thanks for using PhyloPhlAn. Be careful that the FastTree support values are not "

10/3/18

zwol...@gmail.com, Francesco Asnicar5

10/3/18

Error source for downloading the latest version PhyloPhlAn2

Dear Francesco, Thank you very much for your response. I have resolved this question about

unread,

Error source for downloading the latest version PhyloPhlAn2

Dear Francesco, Thank you very much for your response. I have resolved this question about

10/3/18

Curtis Huttenhower

9/4/18

Re: Accession numbers of PhyloPhlan proteins?

Thanks Paul, and good luck with the paper! I think the data you'll need are in the alignments

unread,

Re: Accession numbers of PhyloPhlan proteins?

Thanks Paul, and good luck with the paper! I think the data you'll need are in the alignments

9/4/18

al.lo...@gmail.com, Francesco Asnicar3

6/13/18

pyphlan.py not found

Hello! Thanks for your reply. I answered you in the comments. The problem still exists 13 июня 2018 г

unread,

pyphlan.py not found

Hello! Thanks for your reply. I answered you in the comments. The problem still exists 13 июня 2018 г

6/13/18

Lu Yang, Francesco Asnicar2

5/31/18

error in taxonomy prediction

Hi, Unfortunately the automatic taxonomic prediction in PhyloPhlAn is not working at present. But I

unread,

error in taxonomy prediction

Hi, Unfortunately the automatic taxonomic prediction in PhyloPhlAn is not working at present. But I

5/31/18

5/30/18

problem in generating taxonomy file

On Monday, January 4, 2016 at 10:43:18 AM UTC-5, BFT wrote: Hi, Have you solve this problem? Thanks.

unread,

problem in generating taxonomy file

On Monday, January 4, 2016 at 10:43:18 AM UTC-5, BFT wrote: Hi, Have you solve this problem? Thanks.

5/30/18

beeo...@berkeley.edu, … Francesco Asnicar23

4/9/18

PhyloPhlAn error

Hi Girija, The "LM_phylophlan" text file you obtain is the phylogenetic tree in newick

unread,

PhyloPhlAn error

Hi Girija, The "LM_phylophlan" text file you obtain is the phylogenetic tree in newick

4/9/18

RMondav, Francesco Asnicar2

3/20/18

phylophlan IMG genome set download?

Hi RMondav, We don't have those genomes stored in a genome set collection. I have to say I haven

unread,

phylophlan IMG genome set download?

Hi RMondav, We don't have those genomes stored in a genome set collection. I have to say I haven

3/20/18

Ilnam Kang, Francesco Asnicar3

1/4/18

A problem with usearch version

Your script works nicely!! Thank you very much for your help. Ilnam 2018년 1월 4일 목요일 오후 6시 40분 57초 UTC

unread,

A problem with usearch version

Your script works nicely!! Thank you very much for your help. Ilnam 2018년 1월 4일 목요일 오후 6시 40분 57초 UTC

1/4/18

Curtis Huttenhower, Francesco Asnicar2

10/27/17

Re: number of proteins used in a user tree

Dear Pedro, First of all, many thanks for using PhyloPhlAn. In the PhyloPhlAn folder, you should find

unread,

Re: number of proteins used in a user tree

Dear Pedro, First of all, many thanks for using PhyloPhlAn. In the PhyloPhlAn folder, you should find

10/27/17

Amit Gupta, Francesco Asnicar7

6/21/17

nsegata-phylophlan error

Hi Amit, I'm glad that you managed to get PhyloPhlAn working. Among the ones you mentioned, you

unread,

nsegata-phylophlan error

Hi Amit, I'm glad that you managed to get PhyloPhlAn working. Among the ones you mentioned, you

6/21/17

oona...@gmail.com, Francesco Asnicar3

6/5/17

AttributeError: 'str' object has no attribute 'id'

Hi Francesco, Oh, i see and thanks for your advice! Thanks again for your patient! Ou 2017-06-01 21:

unread,

AttributeError: 'str' object has no attribute 'id'

Hi Francesco, Oh, i see and thanks for your advice! Thanks again for your patient! Ou 2017-06-01 21:

6/5/17

Melanie Smee, Francesco Asnicar12

5/15/17

Error: duplicate keys

Hi Mel, the command you provided is the one for compiling FastTree for Mac and I have never used

unread,

Error: duplicate keys

Hi Mel, the command you provided is the one for compiling FastTree for Mac and I have never used

5/15/17

Nicola Segata, Francesco Asnicar2

3/28/17

Re: PhyloPhlan dev. version error

Hello Naseer, can you provide the complete command you used? And, it was the first time you ran

unread,

Re: PhyloPhlan dev. version error

Hello Naseer, can you provide the complete command you used? And, it was the first time you ran

3/28/17

Yiran Dong, Janet Matsen2

1/8/17

error for assign taxonomy

Hi Yiran. Did you get this sorted out? I am able to run the -u argument on my genome bins, but not

unread,

error for assign taxonomy

Hi Yiran. Did you get this sorted out? I am able to run the -u argument on my genome bins, but not

1/8/17

Search

Clear search

Close search

Google apps

Main menu