Algorithms used in Galaxy

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Algorithms used in Galaxy

Daniyal Kazempour
Dear Galaxy-Developer Team,

my name is Daniyal Kazempour, I am a student of Bioinformatics (5th term) and an undergrad. scientist at the Max Planck Institute of Developmental Biology (Dept.4) in Tübingen.

In our Genomics and Metagenomics seminar we have talked about Galaxy and ran into a question we could not find an answer to (at least pubmed and your website do not provide these information).

In Galaxy it is possible to create a phylogentic tree out of the data from several BLAST results. Now the question that emerges is:

What algorithm(s) is(are) used to create from several BLAST results the phylogenetic trees (or is there some rough description of it available where the principle of it becomes clear?).

And as another question: What does the 'scaling' stand for ? (on phylogenetic trees a 100%----------0% is visible (are that some bias/error rates?))


Many thanks in advance for any hints and

with best regards

Daniyal Kazempour
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Re: Algorithms used in Galaxy

Anton Nekrutenko
Daniyal:

Please take a look at this:


and let mw know if you still have questions.

Thanks,

anton


On Oct 28, 2010, at 5:05 AM, Daniyal Kazempour wrote:

Dear Galaxy-Developer Team,

my name is Daniyal Kazempour, I am a student of Bioinformatics (5th term) and an undergrad. scientist at the Max Planck Institute of Developmental Biology (Dept.4) in Tübingen.

In our Genomics and Metagenomics seminar we have talked about Galaxy and ran into a question we could not find an answer to (at least pubmed and your website do not provide these information).

In Galaxy it is possible to create a phylogentic tree out of the data from several BLAST results. Now the question that emerges is:

What algorithm(s) is(are) used to create from several BLAST results the phylogenetic trees (or is there some rough description of it available where the principle of it becomes clear?).

And as another question: What does the 'scaling' stand for ? (on phylogenetic trees a 100%----------0% is visible (are that some bias/error rates?))


Many thanks in advance for any hints and

with best regards

Daniyal Kazempour
_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev




_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev