Applications and Languages

IBEST maintains dozens of software packages on various servers. This page serves as a quick list by category of the available packages with links to their documentation.

Questions regarding the use of specific software packages should be directed to CRC Staff

IBEST Applications - home brew!

• MiCA Microbial Community Analysis
• ARC Assembly by reduced complexity

Sequence Analysis

• EMBOSS
• G-Language
• PROKKA
• Qiime
• Stacks

Sequence Alignment

• BLAST
• ClustalW
• ClustalX
• Clustal Omega
• Muscle
• HMMER
• Mummer
• PRANK

Read mapping

• BLAT
• Bowtie2

Phylogenetic Inference

• BEAST
• Clann
• ExaML
• Garli
• JModelTest
• MrBayes
• PAML
• PAUP
• Phylip
• Phyml
• RAxML

Population Genetics

• IMA2
• Lamarc
• Migrate
• Structure

Statistical/Mathematical Packages

• R

Contig Assembly

• Cap3
• Phred/Phrap/Consed
• RepeatMasker

Misc

• Avida
• ChimeraSlayer
• Dotur
• NCBI Toolkit
• Mpiblast

Platforms

• Java
• Python
  • Numpy
  • Scipy
• Perl & BioPerl
• Ruby
  • Bioruby

Cluster Tools

• Slurm
• Openmpi
• Modules