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POY - Phylogenetic Analysis Software

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Phylogenetic Analysis of DNA and other data using dynamic homology
Please visit our homepage for more information.

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Buz Wilson, Nick Lucaroni2

11/22/21

POY news anyone?

Development has moved on to PCG. https://github.com/amnh/PCG On Wed, Nov 3, 2021, 8:20 AM Buz Wilson

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POY news anyone?

Development has moved on to PCG. https://github.com/amnh/PCG On Wed, Nov 3, 2021, 8:20 AM Buz Wilson

11/22/21

Leo Borges, Nick Lucaroni2

11/22/21

constraint search

The parser looks like constraint just takes a string as the filename. I am not sure how to apply the

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constraint search

The parser looks like constraint just takes a string as the filename. I am not sure how to apply the

11/22/21

lourd...@gmail.com, Nicholas Lucaroni2

8/15/17

problems with likelihood analisys in POY 5.1.1

Shucks. I had run those functions (newkonnen and brents method) very regularly with large/small

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problems with likelihood analisys in POY 5.1.1

Shucks. I had run those functions (newkonnen and brents method) very regularly with large/small

8/15/17

Lourdes Echevarria

8/15/17

problems with maximum likelihood analysis in POY 5.1.1

Hello, I am running a small analysis to test the performance of POY when running likelihood analysis.

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problems with maximum likelihood analysis in POY 5.1.1

Hello, I am running a small analysis to test the performance of POY when running likelihood analysis.

8/15/17

Buz Wilson, Nick Lucaroni2

1/7/17

Unfortunetly, CUDA isn't free parallelism for software and would require careful consideration

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Unfortunetly, CUDA isn't free parallelism for software and would require careful consideration

1/7/17

Clement Schneider, … Nick Lucaroni11

7/22/16

Compiling poy4 ?

it's probably a gcc issue. we've experienced cmd line options being implicit that weren't

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Compiling poy4 ?

it's probably a gcc issue. we've experienced cmd line options being implicit that weren't

7/22/16

6/15/16

Ubuntu 16.04 & Ocaml

A short note to those using ubuntu 16.04. POY5 generates a segmentation fault after compiling using

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Ubuntu 16.04 & Ocaml

A short note to those using ubuntu 16.04. POY5 generates a segmentation fault after compiling using

6/15/16

Sandra Oliveira

5/31/16

time estimates with rho

Hi! I am using the software Network to estimate the rho ages for some mtDNA haplotypes. When I tried

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time estimates with rho

Hi! I am using the software Network to estimate the rho ages for some mtDNA haplotypes. When I tried

5/31/16

Ivar, … Nicholas Lucaroni5

3/11/16

Trouble downweighting terminal gaps in v.4

The problem is that the parser, that reads your commands (from a file or interactively), had an error

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Trouble downweighting terminal gaps in v.4

The problem is that the parser, that reads your commands (from a file or interactively), had an error

3/11/16

ramiro barrantes, alizoh...@gmail.com2

1/22/16

In making phylogeny of protein superfamily I have 15000+ refseq sequences, many of them very similar to each other. Suggestions for reducing number?

HI Dear You can upload to online servers for analysis. Just download your sequences in Bioedit and

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In making phylogeny of protein superfamily I have 15000+ refseq sequences, many of them very similar to each other. Suggestions for reducing number?

HI Dear You can upload to online servers for analysis. Just download your sequences in Bioedit and

1/22/16

1/22/16

MrBayes Convergence issues ???

Hello Everyone Hope you are doing well Actually, I am new to MrBayes, Before analysis of my data i am

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MrBayes Convergence issues ???

Hello Everyone Hope you are doing well Actually, I am new to MrBayes, Before analysis of my data i am

1/22/16

Leonardo Borges, … Nick Lucaroni7

8/18/15

Not compiling on Yosemite

Those warnings are all fine. It looks like you cancelled early after seeing them? On Aug 18, 2015 11:

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Not compiling on Yosemite

Those warnings are all fine. It looks like you cancelled early after seeing them? On Aug 18, 2015 11:

8/18/15

Ligia, Nick Lucaroni2

6/21/15

interesting. that shouldn't happen -- obviously :). Will run some tests and get back to you soon.

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interesting. that shouldn't happen -- obviously :). Will run some tests and get back to you soon.

6/21/15

Nicholas Lucaroni

3/21/15

Deprecating Google Code

Google is deprecating their google-code service[1] --this forum is not under duress as far as I'm

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Deprecating Google Code

Google is deprecating their google-code service[1] --this forum is not under duress as far as I'm

3/21/15

Ilya Temkin, … Nick Lucaroni5

11/24/14

Segmentation fault 11

hmm, so what changed? OS upgrade? Are you using clang now? nick On Mon, Nov 24, 2014 at 3:35 PM, ilya

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Segmentation fault 11

hmm, so what changed? OS upgrade? Are you using clang now? nick On Mon, Nov 24, 2014 at 3:35 PM, ilya

11/24/14

jan, … Jan De Laet4

11/17/14

problem with POY 5.1.1 on linux

Thanks Nick! I actually like the readline interface better than the ncurses interface (I know, I

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problem with POY 5.1.1 on linux

Thanks Nick! I actually like the readline interface better than the ncurses interface (I know, I

11/17/14

jaakko....@gmail.com, … Nick Lucaroni8

10/18/14

problems with poy 5.1.1 (only unix&win versions)

ah, got things mixed up, even my laptop DOES have two cores in its sole processor and thus installing

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problems with poy 5.1.1 (only unix&win versions)

ah, got things mixed up, even my laptop DOES have two cores in its sole processor and thus installing

10/18/14

9/26/14

POY[4,5] and OCaml 4.02.0+

The issue has been resolved. and in the mercurial repository on google-code. Thankfully it was much

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POY[4,5] and OCaml 4.02.0+

The issue has been resolved. and in the mercurial repository on google-code. Thankfully it was much

9/26/14

Leonardo Borges, … Nick Lucaroni19

9/2/14

FUSE still hanging on paralell

That is kind of weird, though, since we only have and exit() command on the last line and the

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FUSE still hanging on paralell

That is kind of weird, though, since we only have and exit() command on the last line and the

9/2/14

danjanies, Nick Lucaroni2

8/13/14

Error : File "cost_matrix.ml"

That looks to happen when we are trying to find the median of two codes and either of those bit-

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Error : File "cost_matrix.ml"

That looks to happen when we are trying to find the median of two codes and either of those bit-

8/13/14

ajj...@gmail.com, … Nicholas Lucaroni7

6/30/14

Good call. I forgot about the packaged source code. The source I had meant is through the mercurial

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Good call. I forgot about the packaged source code. The source I had meant is through the mercurial

6/30/14

Surangkana Tuanapaya, … Louise Crowley3

4/1/14

cannot import data

Hi Tai, There is a whole section on importing or reading in data in the 'commands.pdf'

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cannot import data

Hi Tai, There is a whole section on importing or reading in data in the 'commands.pdf'

4/1/14

1/8/14

POY5.1.1 released

POY users, We are pleased to announce the release of POY 5.1.1. This is a bug-fix release mainly

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POY5.1.1 released

POY users, We are pleased to announce the release of POY 5.1.1. This is a bug-fix release mainly

1/8/14

Ward C Wheeler, … Nicholas Lucaroni3

11/4/13

POY 5.1 released

Thanks Cyrille, I seem to always forget to update that detail. I've updated all the downloads to

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POY 5.1 released

Thanks Cyrille, I seem to always forget to update that detail. I've updated all the downloads to

11/4/13

Gonzalo Giribet, Nicholas Lucaroni2

11/1/13

Re: [POY] Digest for poy4@googlegroups.com - 1 Message in 1 Topic

Thanks Gonzalo, I should have checked the file sizes before I uploaded an empty zip file. I've

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Re: [POY] Digest for poy4@googlegroups.com - 1 Message in 1 Topic

Thanks Gonzalo, I should have checked the file sizes before I uploaded an empty zip file. I've

11/1/13

Leonardo Borges, Nicholas Lucaroni6

9/19/13

Nick, I have been able to follow the tutorial without problems, but now I am stuck by the lack of a

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Nick, I have been able to follow the tutorial without problems, but now I am stuck by the lack of a

9/19/13

Leonardo Borges, … dha...@mnhn.fr13

9/16/13

Problems with special keys

Thanks a lot, that's an easy one. Cyrille Nicholas Lucaroni <nicholas....@gmail.com>

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Problems with special keys

Thanks a lot, that's an easy one. Cyrille Nicholas Lucaroni <nicholas....@gmail.com>

9/16/13

Ward C Wheeler, b...@optusnet.com.au2

8/16/13

POY 5.0.0 release announcement

Congratulations to the POY5 team!. I am looking forward to compiling this new version and trying it.

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POY 5.0.0 release announcement

Congratulations to the POY5 team!. I am looking forward to compiling this new version and trying it.

8/16/13

Jean-Michel Richer, … Nicholas Lucaroni3

6/3/13

Fitch parsimony how to ?

By default, fasta files are read as unaligned sequence data, stripping out any previous alignment

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Fitch parsimony how to ?

By default, fasta files are read as unaligned sequence data, stripping out any previous alignment

6/3/13

jmric...@gmail.com, Ward C Wheeler2

5/12/13

what does POY stand for as an acronym ?

Hello, Its a meta-acronym, coming from an older program "Yet Another Phylogeny Program"

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what does POY stand for as an acronym ?

Hello, Its a meta-acronym, coming from an older program "Yet Another Phylogeny Program"

5/12/13

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