User:Konrad U Foerstner/Tools and procedures

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

• Newick Utilities
• clann
• phylip
• iTOL
• PhyML

Multiple alignments

• muscle

TSS prediction

• TSSi (untested)

Whole genome alignments

• mauve

Pathway visualization

• iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
• KEGG Mapper (untested)

Transcription Terminator prediction

• TransTerm

miRNA target prediction

miRmap (untested)

Differential gene expression analysis

DESeq

• DeSeq

• small count noise - sequence deeper
• large count noise - sequence more replicates

Others

• BaySEq
• edgR
• Gfold
• NoiSeq

Python

General useful libraries

• BioPython
• bx-python
• NumPy/SciPy
• panda
• statsmodels
• beautiful soup
• matplotlib
• ipython
• PyCogent
• fuzzywuzzy
• pattern
• pysam
• ete2 - For phylogenetic trees

Misc

• Making matplotlib look like ggplot