Boostrapping trees with TASSLE

[Tony Travis]

Hi,

We have using TASSLE to create trees from SNPs as part of a project
investigating drought tolerance in rice. We now want to bootstrap the
trees: Has anyone else done this using TASSLE?

I've considered resampling our SNP data and creating multiple trees
using TASSLE. I'd like to know if this can be done from the TASSLE
command-line as part of the bootstrap and how TASSLE creates trees?

Thanks,

Tony.

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Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
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[Terry Casstevens]

./run_pipeline.pl -fork1 -h mdp_genotype.hmp.txt -tree Neighbor
-export tree -runfork1

./run_pipeline.pl -fork1 -h mdp_genotype.hmp.txt -tree Neighbor
-export tree -exportType Text -runfork1

http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf

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[Tony Travis]

On 07/02/14 15:10, Terry Casstevens wrote:
> ./run_pipeline.pl -fork1 -h mdp_genotype.hmp.txt -tree Neighbor
> -export tree -runfork1
>
> ./run_pipeline.pl -fork1 -h mdp_genotype.hmp.txt -tree Neighbor
> -export tree -exportType Text -runfork1

Hi, Terry.

Thanks for giving me examples of how to create trees from the CLI.

> http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf

And, thanks for the RTFM ;-)

Tony.

[Alex Twyford]

These commands given by Terry won't bootstrap a tree, though? I see in Fei Lu's paper NJ trees are made in TASSEL, then bootstrapped in MEGA--presumably he would have used TASSEL if there were options available?

Alex

[Tony Travis]

On 13/02/14 22:25, Alex Twyford wrote:
> These commands given by Terry won't bootstrap a tree, though? I see in
> Fei Lu's paper NJ trees are made in TASSEL, then bootstrapped in
> MEGA--presumably he would have used TASSEL if there were options available?

Hi, Alex.

I've bootstrapped trees created from bacterial 16S sequence alignments
before, but not from rice SNPs. My question was how does TASSEL create
trees from SNPs (i.e. polymorphism data) and can TASSLE be used to
bootstrap the trees. I'll have a look at Fei Lu's paper.

[Edward S. Buckler]

Hi Folks-

These are great questions.  Bootstrapping a dataset in TASSEL is quite simple, but we generally do it from the level of API.

In TASSEL 5, you use FilterGenotypeTable

 public static FilterGenotypeTable getInstance(GenotypeTable a, int[] subSites) {}

After you decide how to bootstrap your sites, then it takes three lines of code to create the NJ tree.

GenotypeTable aa= FilterGenotypeTable.getInstance(origGenotypeTable, int[] subSites) {}

IBSDistanceMatrix adm = new IBSDistanceMatrix(aa, null);

Tree theTree = new net.maizegenetics.taxa.tree.NeighborJoiningTree(adm);

However, I would comment that phylogenetics is NOT TASSEL’s speciality.  If someone wants to add code to make it better, please just let us know and we will help you out in making these contributions.

-- 
Ed Buckler

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