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Rowan Softley
12/20/23
Pplacer issues with zero likelihood and differing query lengths
Hi, I'm trying to use Pplacer to phylogenetically place V1-V2 16s rRNA fragments into a tree of
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Pplacer issues with zero likelihood and differing query lengths
Hi, I'm trying to use Pplacer to phylogenetically place V1-V2 16s rRNA fragments into a tree of
12/20/23
Cong Xu
2
10/27/20
exception with pplacer
The "nwk" file is end with ");", which is from line 1 character 21593 to line 1
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exception with pplacer
The "nwk" file is end with ");", which is from line 1 character 21593 to line 1
10/27/20
Huda Ghori
,
Erick Matsen
2
8/7/20
no query sequences on ref tree after pplacer step
Please read the manual in greater detail. On Fri, Aug 7, 2020 at 1:44 AM Huda Ghori <hudaghori@
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no query sequences on ref tree after pplacer step
Please read the manual in greater detail. On Fri, Aug 7, 2020 at 1:44 AM Huda Ghori <hudaghori@
8/7/20
Huda Ghori
8/7/20
error with guppy
HI Ive run pplacer on my sequences and when i am converting my tree using the following command:
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error with guppy
HI Ive run pplacer on my sequences and when i am converting my tree using the following command:
8/7/20
Naomi Gilbert
7/18/19
Error message: Fatal error: exception Ppatteries.Sparse.Tokenizer_error(1, 0, _)
Hello, when I run pplacer using the stockholm alignment generated by hmmalign I get the following
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Error message: Fatal error: exception Ppatteries.Sparse.Tokenizer_error(1, 0, _)
Hello, when I run pplacer using the stockholm alignment generated by hmmalign I get the following
7/18/19
Keith Arora-Williams
6/5/19
distmat output ordering
Hi This may be a silly question but do the row and column numbers of the lower triangular matrix put
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distmat output ordering
Hi This may be a silly question but do the row and column numbers of the lower triangular matrix put
6/5/19
Igor Tolstoy
, …
Marc C
6
5/21/19
pplacer on CentOS 7.0
NOTE: My fix above was tested on Ubuntu 16 LTE, not centos. Same goes for my error, though it seems
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pplacer on CentOS 7.0
NOTE: My fix above was tested on Ubuntu 16 LTE, not centos. Same goes for my error, though it seems
5/21/19
Adi Lavy
,
Greg G
4
3/10/19
Is there a way to extract the names of closest references in the tree?
Sorry, you're right, I see now that I have not fully addressed your question. Unfortunately I do
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Is there a way to extract the names of closest references in the tree?
Sorry, you're right, I see now that I have not fully addressed your question. Unfortunately I do
3/10/19
Ramzi Alsallaq
2/7/19
What statistic to use from pplacer to decide on the best reference set among several reference sets?
Dear pplacer developers and community users, I am using several reference data sets that are subsets
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What statistic to use from pplacer to decide on the best reference set among several reference sets?
Dear pplacer developers and community users, I am using several reference data sets that are subsets
2/7/19
abhijeet singh
,
siavash mirarab
2
1/16/19
Reference tree size for a marker gene?
We were able to consistently run it on 1000 species but not 5000. https://www.biorxiv.org/content/
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Reference tree size for a marker gene?
We were able to consistently run it on 1000 species but not 5000. https://www.biorxiv.org/content/
1/16/19
Holly Arnold
, …
Erick Matsen
10
10/22/18
Max OS X Precompiled binaries
Chris-- I don't run OS X, but there appears to be a install_name_tool for doing this sort of
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Max OS X Precompiled binaries
Chris-- I don't run OS X, but there appears to be a install_name_tool for doing this sort of
10/22/18
Greg G
, …
Chris Rosenthal
4
9/20/18
Creating a taxon.db database with taxit
Wonderful, thanks! On Wed, Sep 19, 2018 at 3:17 PM Chris Rosenthal <cros...@gmail.com> wrote:
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Creating a taxon.db database with taxit
Wonderful, thanks! On Wed, Sep 19, 2018 at 3:17 PM Chris Rosenthal <cros...@gmail.com> wrote:
9/20/18
Courtney Smith
,
Erick Matsen
2
6/30/18
error: ...doesnt overlap any reference sequences
Nope! Have you looked at the sequence alignment? On Fri, Jun 29, 2018 at 4:04 PM Courtney Smith <
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error: ...doesnt overlap any reference sequences
Nope! Have you looked at the sequence alignment? On Fri, Jun 29, 2018 at 4:04 PM Courtney Smith <
6/30/18
Erick
6/15/18
Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements
Hello everyone-- The Stamatakis lab has implemented a guppy-like tool, which is described here: https
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Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements
Hello everyone-- The Stamatakis lab has implemented a guppy-like tool, which is described here: https
6/15/18
Ge BoRo
,
Erick Matsen
5
5/25/18
Uncaught exception: Invalid_argument("combine: Different_list_size")
There are some strange things with your files, eg that query file has "no comment" at the
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Uncaught exception: Invalid_argument("combine: Different_list_size")
There are some strange things with your files, eg that query file has "no comment" at the
5/25/18
Alejandra Soto
,
Erick Matsen
3
5/17/18
Filter Pqueries with low likelihood-to-weight ratio
Thank you for the quick response! I am just trying to find a way to do what placeutil did on the old
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Filter Pqueries with low likelihood-to-weight ratio
Thank you for the quick response! I am just trying to find a way to do what placeutil did on the old
5/17/18
Jamie Kwok
, …
Gavin Douglas
7
4/28/18
Uncaught exception: Failure("Internal edge became -4.62762e-07 when attaching subtrees to
Hi Erick, Thanks for the quick reply - ok that's good to know! I'm working on a new version
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Uncaught exception: Failure("Internal edge became -4.62762e-07 when attaching subtrees to
Hi Erick, Thanks for the quick reply - ok that's good to know! I'm working on a new version
4/28/18
andy...@rothamsted.ac.uk
,
Erick Matsen
8
4/4/18
comparison of bwpd between different reference gene trees
Agreed! On Wed, Apr 4, 2018 at 4:46 AM Andy Neal <andy...@rothamsted.ac.uk> wrote: Hello
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comparison of bwpd between different reference gene trees
Agreed! On Wed, Apr 4, 2018 at 4:46 AM Andy Neal <andy...@rothamsted.ac.uk> wrote: Hello
4/4/18
Erick Matsen
3/29/18
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences | bioRxiv
Hello pplacer community-- Please check out this new program: https://www.biorxiv.org/content/early/
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EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences | bioRxiv
Hello pplacer community-- Please check out this new program: https://www.biorxiv.org/content/early/
3/29/18
deth...@stanford.edu
,
Erick Matsen
5
3/22/18
refpkg without tree stats
Thanks again, Erick! Best wishes, Les On 22Mar2018, at 08:38, Erick Matsen <ema...@gmail.com>
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refpkg without tree stats
Thanks again, Erick! Best wishes, Les On 22Mar2018, at 08:38, Erick Matsen <ema...@gmail.com>
3/22/18
Sabeel Mansuri
, …
ctri...@mymail.mines.edu
5
3/8/18
Library Not Loaded
Hi All, I just wanted to update on my progress. I followed Jeff's link and it does indeed allow
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Library Not Loaded
Hi All, I just wanted to update on my progress. I followed Jeff's link and it does indeed allow
3/8/18
ctri...@mymail.mines.edu
,
Erick Matsen
3
3/8/18
Installation help
Hi Erick, Thank you for the reply. I believe I figured it out. It was something silly with how I had
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Installation help
Hi Erick, Thank you for the reply. I believe I figured it out. It was something silly with how I had
3/8/18
lucas...@h-its.org
,
Erick Matsen
3
2/13/18
Guppy fails too late
Hm okay, I see. Was worth a try ;-) On 02/13/2018 09:46 PM, Erick Matsen wrote: Sorry, Lucas, but I
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Guppy fails too late
Hm okay, I see. Was worth a try ;-) On 02/13/2018 09:46 PM, Erick Matsen wrote: Sorry, Lucas, but I
2/13/18
lpi...@berkeley.edu
,
Erick Matsen
3
1/16/18
Didn't find any reference sequences in given alignment file.
It seems that FastTreeDbl might not be outputting the correct labels when I checked with nw_labels. I
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Didn't find any reference sequences in given alignment file.
It seems that FastTreeDbl might not be outputting the correct labels when I checked with nw_labels. I
1/16/18
Michael Doane
,
Erick Matsen
4
12/13/17
merge command
I haven't done this in a while but it looks to me that --split-csv ~/phylogenetic_diversity/
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merge command
I haven't done this in a while but it looks to me that --split-csv ~/phylogenetic_diversity/
12/13/17
Adi Lavy
,
Noah Hoffman
2
11/1/17
Adding taxonomy information when constructing the refpkg
Hi Adi, Ultimately, the mapping of reference sequences included in the refpkg to tax_ids is provided
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Adding taxonomy information when constructing the refpkg
Hi Adi, Ultimately, the mapping of reference sequences included in the refpkg to tax_ids is provided
11/1/17
Michael Doane
,
Erick Matsen
2
10/12/17
rarefy guppy command
This is up to the user. Yes, downsampling to the smallest number of unique sequences is common. On
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rarefy guppy command
This is up to the user. Yes, downsampling to the smallest number of unique sequences is common. On
10/12/17
Jens Preem
, …
Jeff Morris
17
10/2/17
good 16S reference tree for a set of analyses performed on soil bacterial communities
Thanks! Sending now. On Monday, October 2, 2017 at 4:26:12 PM UTC-5, Siavash Mirarab wrote: Jeff, if
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good 16S reference tree for a set of analyses performed on soil bacterial communities
Thanks! Sending now. On Monday, October 2, 2017 at 4:26:12 PM UTC-5, Siavash Mirarab wrote: Jeff, if
10/2/17
Robert Edgar
,
siavash mirarab
2
10/1/17
Existing package for 16S rRNA taxonomy prediction with pplacer?
I have made a SEPP green genes packages available here: https://github.com/smirarab/sepp/tree/master/
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Existing package for 16S rRNA taxonomy prediction with pplacer?
I have made a SEPP green genes packages available here: https://github.com/smirarab/sepp/tree/master/
10/1/17
Michael Doane
,
Erick Matsen
2
9/30/17
Information returned using 'Info' command
Michael-- That's correct. `leaves` is the number of leaves in your reference tree. Re
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Information returned using 'Info' command
Michael-- That's correct. `leaves` is the number of leaves in your reference tree. Re
9/30/17