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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
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fasnicar
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
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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 Asnicar
6
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
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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 Mitsi
4
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
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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 Uppada
3
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/
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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 Asnicar
5
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
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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 Asnicar
8
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?
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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
Lu Yang
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
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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 Asnicar
6
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
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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
Adi Lavy
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
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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 Asnicar
3
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
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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 Park
3
12/5/18
Re: Phylophlan error
good!!!! Malte. thanks. your reply, finally, seriously helpful to me. thanks!!!!! 2015년 10월 5일 월요일 오후
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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 Asnicar
2
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
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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 Asnicar
7
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
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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 Asnicar
11
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
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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 Asnicar
3
10/26/18
Error when use myself database
Thanks. It works when i use input folder. Huifeng Francesco Asnicar <francesc...@gmail.com
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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 Asnicar
2
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 "
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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 Asnicar
5
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
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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
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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 Asnicar
3
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
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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 Asnicar
2
5/31/18
error in taxonomy prediction
Hi, Unfortunately the automatic taxonomic prediction in PhyloPhlAn is not working at present. But I
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error in taxonomy prediction
Hi, Unfortunately the automatic taxonomic prediction in PhyloPhlAn is not working at present. But I
5/31/18
BFT
,
Lu Yang
2
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.
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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 Asnicar
23
4/9/18
PhyloPhlAn error
Hi Girija, The "LM_phylophlan" text file you obtain is the phylogenetic tree in newick
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PhyloPhlAn error
Hi Girija, The "LM_phylophlan" text file you obtain is the phylogenetic tree in newick
4/9/18
RMondav
,
Francesco Asnicar
2
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
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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 Asnicar
3
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
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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 Asnicar
2
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
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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 Asnicar
7
6/21/17
nsegata-phylophlan error
Hi Amit, I'm glad that you managed to get PhyloPhlAn working. Among the ones you mentioned, you
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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 Asnicar
3
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:
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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 Asnicar
12
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
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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 Asnicar
2
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
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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 Matsen
2
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
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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