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.

Contents 1 IBEST Applications - home brew! 2 Sequence Analysis 3 Sequence Alignment 4 Phylogenetic Inference 5 Population Genetics 6 Protein Structure 7 Statistical/Mathematical Packages 8 Contig Assembly 9 Remaining list of all applications and software on IBEST Systems

[edit] IBEST Applications - home brew!

• MiCA Microbial Community Analysis
• HiTSA High Throughput Sequence Analysis
• Statgen Genetic Distances Statistical Generator

[edit] Sequence Analysis

• EMBOSS - Solaris, Clusters

[edit] Sequence Alignment

• BLAST - Solaris, Clusters
• ClustalW - Solaris, Clusters
• ClustalX - Solaris, Clusters
• Muscle Solaris, Clusters
• HMMER - Solaris, Clusters
• Mummer - Solaris, Clusters

[edit] Phylogenetic Inference

• FastDNAml - Solaris, Clusters
• GeneTree - Solaris, Clusters
• Mesquite - Solaris
• ModelTest - Solaris
• MrBayes - Solaris, Clusters
• P4 - Solaris
• PAML - Solaris, Clusters
• PAUP - Solaris, Clusters
• Seq-Gen - Solaris, Clusters
• Phylip - Solaris, Clusters
• RAxML RAxML web
• TreeView - Solaris, Clusters

[edit] Population Genetics

• GeneConv - Solaris
• Fluctuate - Solaris, Clusters
• Lamarc - Solaris, Clusters
• Migrate - Solaris, Clusters
• Recombine - Solaris
• Structure - Solaris

[edit] Protein Structure

• Xplor - Clusters
• Amber7 - Solaris, Clusters
• Charmm - Solaris, Clusters
• Cn3d - Windows

[edit] Statistical/Mathematical Packages

• Gromacs - Clusters
• Mathematica - Solaris
• MatLab - Solaris
• R - All
• S3 (Stochastic Spatial Simulator) - Solaris, Clusters

[edit] Contig Assembly

• Phred/Phrap/Consed - Solaris, Clusters
• RepeatMasker - Solaris, Clusters
• Cap3

[edit] Remaining list of all applications and software on IBEST Systems

• Software