User: Arjen Ten Have
Arjen Ten Have • 340
- Reputation:
- 340
- Status:
- Trusted
- Location:
- Mar del Plata Argentina
- Last seen:
- 1 year, 4 months ago
- Joined:
- 8 years ago
- Email:
- t************@gmail.com
Posts by Arjen Ten Have
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... Does anybody know how to install the SCI-PHY 3 phylogenomics package from Berkely. It seems the configure script is lacking. It is a C or C++ package ...
written 22 months ago by
Arjen Ten Have • 340
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... Are you sure? I understood bLast is local since it is based on perfect,
hence local matches that are extended to HSSPs that then become connected
by a NW. It doesn't make sense to use SW since alignment between the HSSPs
is from 0,0 to n,m where 0,0 corresponds with the first position following
HSSP ...
written 23 months ago by
Arjen Ten Have • 340
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... The title covers most of it. I want to run MrBayes chains on a machine equipped with a KeplerK40 GPU. I am very confused regarding the dependencies. Beagle seems to be a package for likelihood calculations on GPU but it is not clear how this works on multi GPU devices such as the kepler k40. Intuiti ...
written 3.4 years ago by
Arjen Ten Have • 340
• updated
17 months ago by
Biostar ♦♦ 20
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... I am going thru my lectures for next month postgrad course and ran into a doubt. To me it would make sense to apply Needleman-Wunsch (Global) when aligning the subsequences in between the HSSPs identified in the earlier steps. But my class (which I made a couple of years ago) actually states it uses ...
written 4.2 years ago by
Arjen Ten Have • 340
• updated
2.0 years ago by
mfilipav • 0
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... Thanks for all the comments. As a follow up question something that I cannot get clear: Memory and communication speed. So the third generation Tesla GPUs (Kepler) are equipped with on board memory. The K40 has like 12Gb, the K20 has 5Gb. In my experience, memory is always limiting but I have no clu ...
written 4.3 years ago by
Arjen Ten Have • 340
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... Indeed the idea is to implement it into an existing cluster of the physics
department, they have a technician in charge. Presume he will take care of
the technical details. I intend to use it with existing software that is
well supported for CUDA such as PHYML and MrBayes (via Beagle), MAFFT and
AMB ...
written 4.3 years ago by
Arjen Ten Have • 340
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... I want to buy a GPU in order to obtain more computing power. This is not such an easy thing here in Argentina since I need to import it, which goes with about 2 kg of paperwork, and since funding is limited I want to do it right. Thus far I came to the option of buying a single Kepler K40 GPU accele ...
written 4.3 years ago by
Arjen Ten Have • 340
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Answer:
A: 50% credibility Bayesian tree
... Thanks for the clear and complete answer!
...
written 4.5 years ago by
Arjen Ten Have • 340
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... I ran a Bayesian tree on Mr Bayes. Once convergence was reached I started to look at the trees. I first checked the standard output. Topology was more or less identical to the ML tree I obtained with PHYML but certain distances were really weird. Than I ran a consensus made of all compatible trees a ...
written 4.5 years ago by
Arjen Ten Have • 340
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... My question is more directed at whether it will work for divergent datasets...
...
written 5.0 years ago by
Arjen Ten Have • 340
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For Script To Calculate A Distance Matrix Based On Tree File
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For Manual Msa Editor
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For Script To Calculate A Distance Matrix Based On Tree File
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For Script To Calculate A Distance Matrix Based On Tree File
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