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Last active May 24, 2016 17:05
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BioNotes.md

DNA-DNA Hybridization

TODO

Restriction Enzyme Digestion Profiles

TODO

Genetic Mapping

Can offer firm evidence if a disease transmitted from parent to child is linked to one or more genes. Provides clues about which chromosome contains the gene and where it is on the chromosome.

Mapping or positioning the primary library (cosmid, BAC, YAC) is carried out using a combination of techniques such as:

Genetic Marker Identification

TODO

Raw
err.md

PrimerProspector

TypeError: range() integer end argument expected, got numpy.float64.

https://groups.google.com/forum/#!topic/qiime-forum/Ip6xyAC4QS4

From some prior tests, it is a conflict between versions of matplotlib and numpy, try using these versions: Matplotlib 1.2.1 numpy 1.7.1 and see if that fixes the issue.

Raw
libraries.md

HPC

  • ViennaCL ViennaCL is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports CUDA, OpenCL, and OpenMP (including switches at runtime).

Visualization

  • PAUP PAUP* (Phylogenetic Analysis Using Parsimony and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implemented parsimony, but from version 4.0 (when the program became known as PAUP) it also supports distance matrix, and likelihood methods.
  • IQ-TREE
  • fasttree
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