Computational Biology, Bioinformatics and Cheminformatics



Overview

mouseorisit 

SRA domain of mouse Np95 in
complex with DNA (PDB: 2ZKE)
(Image Credit: Dr. Ryan Johnson,
UNM CARC)

CARC supports a wide array of open source and licensed bioinformatics, computational biology, and cheminformatics software on its supercomputing clusters. These include codes for phylogenetic analysis; genomics (sequence alignment, mapping, and processing, SNP/SNV identification, and de novo assembly); molecular dynamics and QM/MM simulation; cheminformatics; and molecular visualization tools. 

Large shared genomic and other databases in regular use by members of a research group can be migrated to and stored on CARC filesystems or on the Research Storage Consortium (RSC) mass storage system. To submit a shared storage request see Special Requests

Custom-designed workshops for specific codes or workflows can be designed in collaboration with CARC Applications Scientists and Systems staff. For inquiries, please contact director@carc.unm.edu

Code/ Software Suite

Purpose

Installed Versions

Machines
Abyss Sequence assembly 1.3.4, 1.5.2 nano, poblano, Ulam
AmpliconNoise Noise removal from PCR amplicons 1.9.1

nano, Metropolis, Ulam, Galles

AutoDock Molecular docking 4.2.6

Ulam, Xena

AutoDock Vina Molecular docking 1.1.2

Ulam, Xena

BarraCUDA GPU Accelerated DNA Sequence Alignment. Based on BWA 0.7.0

Xena

BEAGLE Bayesian genotype analysis for large-scale genetic data 2.1 Ulam, nano
BEAST MCMC Bayesian sequence analysis  1.8.2, 2.2.0 Ulam, nano
Bowtie Sequence alignment 0.12.8, 2.1.0, 2.2.3 nano, pequena, Gibbs
BWA Mapping low-divergent sequences 0.7.12 Ulam, nano
CNVer Copy number variation detection 0.8.1 Ulam
Cufflinks Sequence assembly 2.1.1 nano, Gibbs
FastQC Quality control on high throughput sequence data 0.11.3 Ulam, nano
FASTX_Toolkit FASTA/FASTQ file preprocessing 0.0.13.2 nano, pequena, Metropolis
GATK Genome analysis 3.3-1 Ulam
GARLI Heuristic phylogenetic searches  2.01 Metropolis
GMAP Genomic Mapping and Alignment 2012-06-12 pequena
GSNAP Sequence alignment 2013-04-14, 2013-07-14, 2013-09-11, 2013-11-23 nano, poblano, Metropolis, Ulam, Galles
LASTZ Sequence alignment 1.02 nano, Ulam
MEGAN Metagenomic analysis 4.40.3 pequena
MetaVelvet Metagenomic assembly 1.2.01, 1.2.02 pequena, Ulam
Migrate-n Migrational gene flow modeling  3.5.1 nano
MrBayes Bayesian inference of phylogeny 3.2.2, 3.2.4 nano, Metropolis, Ulam
MSVAR MCMC genealogical history estimation 1.3 nano
Muscle Sequence alignment 3.8.1 nano, Ulam
PAML Phylogenetic analysis  4.8 Ulam, nano
Pindel Genomic analysis; insertion/deletion detection 09.22.14 nano, Ulam
PRISM Split read mapping 1.1.6 nano, Gibbs, Metropolis, Ulam
pyRAD RADseq-like data analysis 2.15 nano, Ulam
QIIME Microbiome analysis 1.9.1 nano, Metropolis, Ulam, Galles, pequena
RAxML Parallel phylogenetic inference 8.1.17 nano, Ulam
SAMStat SAM/BAM sequence analysis   1.08 pequena 
SAMTools Sequence alignment and mapping 0.1.19, 1.1 nano, Gibbs, Ulam
Seqtk FASTA/FASTQ processing 1.0-r31 nano, pequena, Metropolis
TopHat Splice junction mapper 2.0.9, 2.0.10 nano
USEARCH Sequence analysis 7.0.1090 nano, Ulam
Velvet Short read sequence assembly 1.2.08, 1.2.10 nano, pequena, Gibbs, poblano, Metropolis, Ulam, Galles

To request additional software installation please email help@carc.unm.edu

Center for Advanced Research Computing

MSC01 1190
1601 Central Ave. NE
Albuquerque, NM 87106

p: 505.277.8249
f:  505.277.8235
e: