Bremer support

[Robert Stephens]

Hi,

I'm new to poy4. To analyze my phenotype-genotype data, I customized
tutor scripts from poy4 manual. Bootstrap and Jackknife work great as
does the first half of Bemer support script. However, the second part
of Bremer lists the same error number at each node of a pdf tree file
for all 124 nodes. Is there a work around or do I download a
correction? I went back to 2007 in the archives. I've had my copy of
poy 4.1.2 for about 3 wks.

Is there a reference or help file for basics on reading my diagnosis
file?

I notice when I change wt. for a phenotypic character using Hennig86
poy4 picks upon it but not when I set the ccode to all 77 phenotypic
characters unordered.


Any info to my three problems will be very helpful to me.

Thanks,

Bob

[Ward Wheeler]

Hello,

Could you paste teh error?

Did you try to input a pdf file into poy?

I'm new to poy4.  To analyze my phenotype-genotype data, I customized
tutor scripts from poy4 manual.  Bootstrap and Jackknife work great as
does the first half of Bemer support script.  However, the second part
of Bremer lists the same error number at each node of a pdf tree file
for all 124 nodes.  Is there a work around or do I download a
correction?  I went back to 2007 in the archives.  I've had my copy of
poy 4.1.2 for about 3 wks.

Which format did you use?  xml?

 

Is there a reference or help file for basics on reading my diagnosis
file?

Could you paste the commands?

 

I notice when I change wt. for a phenotypic character using Hennig86
poy4 picks upon it but not when I set the ccode to all 77 phenotypic
characters unordered.

W

 

Any info to my three problems will be very helpful to me.

Thanks,

 Bob

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Ward Wheeler
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192
USA
whe...@amnh.org
http://research.amnh.org/scicomp/ward_wheeler.html

[Robert Stephens]

Hi,

I attached the Bremer .pdf file. The error number also appeared at the end of the Results and Errors half of the output file. 

I worked out my Hennig86 ccode problem 

but I need more time to mull over the diagnosis after reading and studying the all_trees log file to frame a better question.

Is it expected that all Hennig86 files have unordered characters for POY4 or is it the investigator's decision to have all or a mix of ordered/unordered characters?

Thanks,

Bob

[ward wheeler]

Hello,

I attached the Bremer .pdf file. The error number also appeared at the end of the Results and Errors half of the output file. 

They're not errors as much as the initial value that was not updated during the Bremer search--what was your input tree?  Was it a pdf file?  IF so, that's the problem.

Should have been newick.

Is it expected that all Hennig86 files have unordered characters for POY4 or is it the investigator's decision to have all or a mix of ordered/unordered characters?

The default for Hennig86 (and Nona and TNT and POY but NOT Nexus) is ordered.  Anything else must be specified.

W

<Treesgrf.pdf>

Ward Wheeler

Division of Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024-5192

USA

whe...@amnh.org

http://research.amnh.org/scicomp/ward_wheeler.html

http://research.amnh.org/scicomp/projects/poy.php

[Robert Stephens]

Hi,

I'll give my B related  files a closer review.

Thanks. 

Bob