[Mesquitelist] sampling and resampling

[Wayne Maddison]

This could probably done by scripting, but it would be complex.  I'll 
look into the possibility of a new module that could supply a matrix 
that is the concatenation of other matrices, and it would be up to 
you to choose rarefactions for those other matrices.  If it's easy to 
make, then this new module may be available within the next month or 
two.

Wayne

At 11:11 AM -0500 9.12.2008, James Schulte wrote:
>Hello Mesquite Users,
>
>I have a general inquiry as well as perhaps a specific request for
>future versions of Mesquite.
>
>I have a multigene dataset with 7 nuclear genes, all of which are
>over 1200 bp and a few between 2-3 kb.  What I would like to do is to
>test alternative strategies of data sampling for large multiple
>nuclear gene based projects.  That is, is it better to get lots (>10)
>of smaller gene fragments (~<700 bp) or use fewer (<10) larger gene
>fragments (~>1200) to reconstruct a robustly supported tree for a
>particular group.
>
>What I would like to do is to take my dataset with 7 genes and ~11500
>bp and rarefy it to make several new datasets that are composed of
>difference sized rarefied "genes".  So, for example, I would like to
>make 100 new datasets, each 10000 bp that are made up of twenty 500bp
>"fragments/gene regions" from the larger dataset.  Or make 100
>datasets 10kb that are each made up of five 2000 bp "fragments/gene
>regions". At the moment, I can make a single set of 100 datasets with
>a "gene" of a particular size using the rarefy option and batch
>architecture but what I haven't been able to figure out, and I'm not
>sure if Mesquite can do this yet, is if I can easily concatenate
>those 100 datasets with 100 other datasets of another "gene".
>
>I hope this is making at least a little bit of sense and I very much
>appreciate any advice anyone may have.
>
>Best regards,
>Jim
>
>
>James A. Schulte, II
>Department of Biology
>177 Clarkson Science Center, MRC 5805
>8 Clarkson Avenue
>Clarkson University
>Potsdam, NY  13699-5805
>Phone:  315-268-4401
>Fax:  315-268-7118
>
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-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416

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