User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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== Phylogenetic trees == | == Phylogenetic trees == | ||
* [http://cegg.unige.ch/newick_utils Newick Utilities | * [http://cegg.unige.ch/newick_utils Newick Utilities] | ||
* [http://bioinf.nuim.ie/clann/ clann] | * [http://bioinf.nuim.ie/clann/ clann] | ||
* [http://evolution.genetics.washington.edu/phylip.html phylip] | * [http://evolution.genetics.washington.edu/phylip.html phylip] | ||
Revision as of 10:56, 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
