User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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* Important. Base alignment quality (BAQ) is switched on per default and very (too) strict [http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html 5 Things to Know About SAMtools Mpileup] | * Important. Base alignment quality (BAQ) is switched on per default and very (too) strict [http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html 5 Things to Know About SAMtools Mpileup] | ||
== Phylogenetic trees == | |||
== Multiple alignments == | |||
* [http://www.drive5.com/muscle/ muscle] | |||
Revision as of 10:46, 17 December 2012
SNP calling
With Samtools
- Important. Base alignment quality (BAQ) is switched on per default and very (too) strict 5 Things to Know About SAMtools Mpileup
Phylogenetic trees
Multiple alignments
TSS prediction
- TSSi (untested)
Whole genome alignments
Pathway visualization
- iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
- KEGG Mapper (untested)
Trascription Terminator prediction
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- panda
- statsmodels
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
