[Biojava-l] How to get guide tree,root MSA and lineage file

[Andreas Prlic]

Hi Muhammad,

not sure if you are talking about biojava... The alignment module
currently does not print out this internal data, but it should be easy
to add. Take a look at the GuideTree class for example. The alignment
module is using the forester library for some of the calculations,
wich might provide some additional utility methods which you might
find useful.

Andreas



On Fri, Feb 24, 2012 at 3:41 AM, Muhammad Tariq Pervez
<tariq_cp at hotmail.com> wrote:
>
> hi all,
> I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc.
> Your help will be very beneficial for the research work.
>
> Best Regards.
>
>
> Muhammad Tariq Pervez
>
> Ph.D (Bioinformatics Scholar)
>
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