[ccp4bb] Summary: Phylogenetic analysis??

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: CCP4i: P212121 to P22121 conversion
From: Jacob Wong jacob {- dot -} j {- dot -} wong {- at -} GMAIL {- dot -} COM
Date: 2008-11-08

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Subject: Re: CCP4i: P212121 to P22121 conversion
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2008-11-09

Subject: Summary: Phylogenetic analysis??
From: Raji Edayathumangalam raji {- at -} BRANDEIS {- dot -} EDU
Date: 2008-11-09

Hi Everyone,

Since some folks have been asking me, below is my original question
and here's a summary of the responses. I had already googled a bunch
of these links before posting to ccp4bb but still lots of useful info
in responses, as always!

Raji

====================
DNAStar will do this if you have a copy lying around.
Gabriel Birrane

T-coffee
http://www.ebi.ac.uk/Tools/t-coffee/index.html
Graeme Garvey

HI Raji,
~15 years ago I remember using treetool on a solaris system to flip
nodes of a tree to alter the groupings. I am not sure what the
current tools are that people use, but it looks
like the old sparc treetool package is archived on
http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/unix/GDE/
treetool/
It looks like development stopped in 1995, there is a debeian/linux
version --
http://packages.debian.org/unstable/science/treetool and it may also
be included
with GDE as part of the BIRCH system now --
http://home.cc.umanitoba.ca/~psgendb/treetool/treetool.html
However, searching for treetool, I also found a list of other tree
manipulation tools here
http://evolution.genetics.washington.edu/phylip/
software.html#Interactive
Perhaps one of the newer programs will work for you
Mitchell Miller

Some suggestions:
1)download your PSI-BLAST hits in FASTA format
2)align the sequences using PRANK http://www.ebi.ac.uk/goldman-srv/
prank/prank/
3a)Use BEAST to evaluate the phylogeny http://beast.bio.ed.ac.uk/ and/or
3b)Use MrBayes to evaluate the phylogeny http://mrbayes.csit.fsu.edu/
4)Use FigTree to examine the BEAST or MrBayes output tree http://
tree.bio.ed.ac.uk/software/figtree/
Starr Hazard

Hi Raji..I am assuming you have looked at the "Blast Link section" on
NCBI called BLINK..You can filter by Archaea , Eukarya , Prokarya in
the least..
You can find a screencast video describing Blink at
http://www.bioscreencast.com/html/tag/blink
Or the actual documentation at
http://www.ncbi.nlm.nih.gov/sutils/static/blinkhelp.html#SampleQuestions
Its good to look for homologs this way
Another good tree viewer and manipulator is jalview check it out or
check out
http://www.bioscreencast.com/html/tag/jalview
Hope this helps
Hari Jayaram

I had to create the tree of life for a bioinformatics class recently.
Download the ribosomal rna sequences for the species you're
interested in from http://www.arb-silva.de/browser/, you can use
their aligner or you can align them yourself (clustalw or pick your
favorite), then I used raxml (doi:10.1093/bioinformatics/bti191 ) to
make the trees and then you can visualize the trees in something like
HyperTree (Mac). Don't know of any PC alternatives as it's not my
main OS.
HTH
Francis Reyes
=====================

Original question:

> Hi Everyone,
>
> Could someone please tell me how to display the evolutionary/
> phylogenetic tree of the homologs of my protein of interest.
>
> When I perform a PSI-BLAST search for my protein, I receive about
> 130 top hits for homologs. The NCBI or EBI tools that I've laid my
> hands on seem to only display a 'phylogenetic' tree based on the
> distance relationships between the protein sequences and that is
> not what I am after. I'd like to find a way to resort the results
> and redisplay a tree that say progresses from, say 'yeast to
> human'. What I have now is the organisms shown in some random
> order, say, rat followed by C. elegans followed by human. I am
> going bonkers trying to find a simple way to do what I want.
>
> Thanks and sorry for this Bioinformatics101-type question.
> Raji

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: CCP4i: P212121 to P22121 conversion
From: Jacob Wong jacob {- dot -} j {- dot -} wong {- at -} GMAIL {- dot -} COM
Date: 2008-11-08

Next message:
Subject: Re: CCP4i: P212121 to P22121 conversion
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2008-11-09