protein

[Emanuelle Corrêa]

I am analyzing a data set of proteins and this what I am doing

 

read the file

transform tcm1,1

build 2000

select

swap

implied alignment

save trees

 

Then I recover the implied alignment in another phylo program, build the tree again for some diagnosis.

 

Questions:

In the case of aminoacids, how are gaps treated?

transform command works for aminoacids?

When I transform I change from dinamic to static homology, so to get the implied alignment I need to read the file and the tree again without transformations...is this a valid procedure?

 

Thanks in advance for the information

 

 

[Cyrille D'Haese]

Dear all,

I'm about to install POY4 on my cluster (17 nodes, 2 Go Ram per node, 22
AMDs 64 bits CPUʼs for the slave nodes and 4 Xeon 32 bits CPUʼs for the
two master nodes).
Any tips before I start?
Which flavor of mpi should I use?
The catch is that we use a queuing system (SGE GridEngine). Does this
create problems?

Thanks!

Cyrille

--
Cyrille D'Haese

UMR 5202 CNRS
"Origine, Structure et Evolution de la Biodiversité"
Département Systématique et Evolution
Muséum National d'Histoire Naturelle
CP50 - Entomologie
45 rue Buffon, 75231 Paris cedex 05, FRANCE

Voice: +33 (0)1 40 79 57 36
Fax: +33 (0)1 40 79 56 79
e-mail: dha...@mnhn.fr

[Andres Varon]

Hello Cyrille,

This is probably too late but ....

On Apr 29, 5:40 am, "Cyrille D'Haese" <dha...@mnhn.fr> wrote:
> Dear all,
>
> I'm about to install POY4 on my cluster (17 nodes, 2 Go Ram per node, 22
> AMDs 64 bits CPUʼs for the slave nodes and 4 Xeon 32 bits CPUʼs for the
> two master nodes).
> Any tips before I start?
> Which flavor of mpi should I use?

Both MPICH and OpenMPI are quite good. I have had good no issues with
either one of them.

> The catch is that we use a queuing system (SGE GridEngine). Does this
> create problems?

No problems to my knowledge. And I don't see any reason to have any.
As far as POY knows, the scheduler doesn't even exists.

best,

Andres