User: Arjen Ten Have

gravatar for Arjen Ten Have
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340
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Location:
Mar del Plata Argentina
Last seen:
1 year, 4 months ago
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8 years ago
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Posts by Arjen Ten Have

<prev • 37 results • page 1 of 4 • next >
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Cannot install SCI-PHY v3, configure script lacking?
... 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 ...
phyogenomics written 22 months ago by Arjen Ten Have340
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Comment: C: Is BLAST using Needleman-Wunsch or Smith-Waterman when aliging in between HSSPs?
... 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 Have340
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MrBayes on Kepler K40 GPU: What dependencies do I need? Beagle, MPI or both?
... 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 ...
myposts written 3.4 years ago by Arjen Ten Have340 • updated 17 months ago by Biostar ♦♦ 20
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Is BLAST using Needleman-Wunsch or Smith-Waterman when aliging in between HSSPs?
... 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 ...
blast written 4.2 years ago by Arjen Ten Have340 • updated 2.0 years ago by mfilipav0
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Answer: A: GPU implementation Tesla Kepler accelerator?
... 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 Have340
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Comment: C: GPU implementation Tesla Kepler accelerator?
... 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 Have340
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GPU implementation Tesla Kepler accelerator?
... 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 ...
gpu server written 4.3 years ago by Arjen Ten Have340
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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 Have340
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50% credibility Bayesian tree
... 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 ...
phylogeny mrbayes consensus tree written 4.5 years ago by Arjen Ten Have340
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Answer: A: Bayesian Phylogeny For Very Divergent Dataset?
... My question is more directed at whether it will work for divergent datasets... ...
written 5.0 years ago by Arjen Ten Have340

Latest awards to Arjen Ten Have

Popular Question 22 months ago, created a question with more than 1,000 views. For Script To Calculate A Distance Matrix Based On Tree File
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Manual Msa Editor
Popular Question 3.0 years ago, created a question with more than 1,000 views. For 50% credibility Bayesian tree
Student 3.0 years ago, asked a question with at least 3 up-votes. For Manual Msa Editor
Great Question 3.4 years ago, created a question with more than 5,000 views. For Script To Calculate A Distance Matrix Based On Tree File
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Manual Msa Editor
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Script To Calculate A Distance Matrix Based On Tree File
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Script To Calculate A Distance Matrix Based On Tree File
Appreciated 5.0 years ago, created a post with more than 5 votes. For C: Is Biostar Killing The Bioinformatics Core?
Pundit 5.0 years ago, created a comment with more than 10 votes. For C: Is Biostar Killing The Bioinformatics Core?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Script To Calculate A Distance Matrix Based On Tree File
Commentator 5.0 years ago, created a comment with at least 3 up-votes. For C: Is Biostar Killing The Bioinformatics Core?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Build A Tree Out Of 10000 Mitochondrial Sequences.
Student 5.0 years ago, asked a question with at least 3 up-votes. For How To Demonstrate Long Branch Attraction

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