Bioinformatics Software

A lot of Bioinformatics software can now be installed via Anaconda Python. These packages can be accessed on all MCSR systems by loading the main Python module and loading the bioinf environment. These packages are listed below. All other Bioinformatics software is listed on the main documentation page.

To use the bioinf environment:

module load python
source activate bioinf

The packages installed in the bioinf environment include:

• ALE
• ARAGORN
• Bandage
• bcftools
• BioPerl
• BLAST
• bowtie2
• Canu
• cd-hit
• CheckM
• Deepbinner
• DeepBGC
• EMBOSS
• FastANI
• FGMP
• Filtlong
• FMLRC
• freebayes
• GMAP/GSNAP
• HMMER
• htseq
• iqtree
• MetaBGC
• MetaPhlAn2
• mothur
• MUMmer
• MUSCLE
• MultiQC
• NumPy
• PANDAS
• Prodigal
• Prokka
• RAxML
• SAMtools
• SciPy
• Sickle
• SPAdes
• VSEARCH