pplacer users

Hi everyone-- Pplacer just got an upgrade in its conda installation process. It now uses a recent

Hello Zhu-- Are you just doing placement, or are you also doing taxonomic classification? If it's

Hi, I'm trying to use Pplacer to phylogenetically place V1-V2 16s rRNA fragments into a tree of

The "nwk" file is end with ");", which is from line 1 character 21593 to line 1

Please read the manual in greater detail. On Fri, Aug 7, 2020 at 1:44 AM Huda Ghori <hudaghori@

HI Ive run pplacer on my sequences and when i am converting my tree using the following command:

Hello, when I run pplacer using the stockholm alignment generated by hmmalign I get the following

Hi This may be a silly question but do the row and column numbers of the lower triangular matrix put

NOTE: My fix above was tested on Ubuntu 16 LTE, not centos. Same goes for my error, though it seems

Sorry, you're right, I see now that I have not fully addressed your question. Unfortunately I do

Dear pplacer developers and community users, I am using several reference data sets that are subsets

We were able to consistently run it on 1000 species but not 5000. https://www.biorxiv.org/content/

Chris-- I don't run OS X, but there appears to be a install_name_tool for doing this sort of

Wonderful, thanks! On Wed, Sep 19, 2018 at 3:17 PM Chris Rosenthal <cros...@gmail.com> wrote:

Nope! Have you looked at the sequence alignment? On Fri, Jun 29, 2018 at 4:04 PM Courtney Smith <

Hello everyone-- The Stamatakis lab has implemented a guppy-like tool, which is described here: https

There are some strange things with your files, eg that query file has "no comment" at the

Thank you for the quick response! I am just trying to find a way to do what placeutil did on the old

Hi Erick, Thanks for the quick reply - ok that's good to know! I'm working on a new version

Agreed! On Wed, Apr 4, 2018 at 4:46 AM Andy Neal <andy...@rothamsted.ac.uk> wrote: Hello

Hello pplacer community-- Please check out this new program: https://www.biorxiv.org/content/early/

Thanks again, Erick! Best wishes, Les On 22Mar2018, at 08:38, Erick Matsen <ema...@gmail.com>

Hi All, I just wanted to update on my progress. I followed Jeff's link and it does indeed allow

Hi Erick, Thank you for the reply. I believe I figured it out. It was something silly with how I had

Hm okay, I see. Was worth a try ;-) On 02/13/2018 09:46 PM, Erick Matsen wrote: Sorry, Lucas, but I

It seems that FastTreeDbl might not be outputting the correct labels when I checked with nw_labels. I

I haven't done this in a while but it looks to me that --split-csv ~/phylogenetic_diversity/

Hi Adi, Ultimately, the mapping of reference sequences included in the refpkg to tax_ids is provided

This is up to the user. Yes, downsampling to the smallest number of unique sequences is common. On

Thanks! Sending now. On Monday, October 2, 2017 at 4:26:12 PM UTC-5, Siavash Mirarab wrote: Jeff, if