POD Software Information

JupyterHub Server

Python Notebook Server

Available on all compute servers

https://<server_name>.ccbb.utexas.edu
for example:

• https://gsafcomp02.ccbb.utexas.edu

Python 3.9

About R and R Studio Server 

RStudio Server

RStudio Web Interface

R 4.3.1

About Python and JupyterHub server 

build-essential

gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool

emacs, vi, vim, ed

text editors

postfix

mail programs

perl

perl interpretor

python 2

python version 2 interpretor

python 3

python version 3 interpretor

ruby

ruby programming language

samba

Windows SMB/CIFS file and printer sharing protocol and applications

screen, tmux

Text window managers (multiplexer)

ssh

Secure Shell (remote access)

sudo

Root access for POD delegates only

tar

File archiving utility

wget, curl

Remote file/url transfer utilities

gzip, zip, unzip

File compression and archiving tools.

scons

Software build tool

swig

Software development tool

sqlite3

SQL Lite databases

git

Version control utilities

abyss

2.0.2-3

de novo, parallel, sequence assembler for short reads

bamtools

2.4.1+dfsg-2

toolkit for manipulating BAM (genome alignment) files

bedtools

2.26.0+dfsg-5

suite of utilities for comparing genomic features

bioperl

1.7.2-2

Perl tools for computational molecular biology

bioperl-run

1.7.1-3

BioPerl wrappers: scripts

blast2

1:2.6.0-1

Basic Local Alignment Search Tool

bowtie

1.2.2+dfsg-2

Ultrafast memory-efficient short read aligner

bowtie2

2.3.4.1-1

Ultrafast memory-efficient short read aligner

bwa

0.7.17-1ubuntu0.1

Burrows-Wheeler Aligner

cd-hit

4.6.8-1

a suite of programs designed to quickly group sequences

clustalw

2.1+lgpl-5

No description

clustalx

2.1+lgpl-6

No description

cufflinks

2.2.1+dfsg.1-2

Transcript assembly, differential expression and regulation for RNA-Seq

diamond

2.0.14

sequence aligner for protein and translated DNA searches

DiffBind

3.0.15

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data

ea-utils

1.1.2+dfsg-4build1

command-line tools for processing biological sequencing data

emboss

6.6.0+dfsg-6build1

european molecular biology open software suite

emboss-lib

6.6.0+dfsg-6build1

EMBOSS Libraries

fastdnaml

1.2.2-12

Tool for construction of phylogenetic trees of DNA sequences

fastqc

0.11.5+dfsg-6

A quality control application for high throughput sequence data

fastx-toolkit

0.0.14-5

FASTQ/A short nucleotide reads pre-processing tools

hmmer

3.1b2+dfsg-5ubuntu1

profile hidden Markov models for protein sequence analysis

jaligner

1.0+dfsg-4

Smith-Waterman algorithm with Gotoh’s improvement

jellyfish

2.2.8-3build1

count k-mers in DNA sequences

khmer

2.1.2+dfsg-3

k0.7.17-1ubuntu0.1-mer counting, filtering and graph traversal

libbiojava-java

1:1.7.1-7

Java API to biological data and applications (default version)

libbiojava-java-demos

1:1.7.1-7

Example programs for BioJava

macs

2.1.1.20160309-2

Model-based Analysis of ChIP-Seq on short reads sequencers

mafft

7.310-1

Multiple alignment program for amino acid or nucleotide sequences

maq

0.7.1-7

maps short fixed-length polymorphic DNA sequence reads to reference sequences

med-bio

3.0.1ubuntu1

Debian Med bioinformatics packages

med-cloud

3.0.1ubuntu1

Debian Med bioinformatics applications usable in cloud computing

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

minfi

1.24.0

Analyze Illumina Infinium DNA methylation arrays

mothur

1.39.5-2build1

sequence analysis suite for research on microbiota

mothur-mpi

1.39.5-2build1

mpi-enabled binary for mothur

mrbayes-mpi

3.2.6+dfsg-2

Bayesian Inference of Phylogeny – mpi version

mummer

3.23+dfsg-3

Efficient sequence alignment of full genomes

muscle

1:3.8.31+dfsg-3

Multiple alignment program of protein sequences

ncbi-blast+

2.6.0-1

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy

2.6.0-1

NCBI Blast legacy call script

ncbi-seg

0.0.20000620-4

tool to mask segments of low compositional complexity in amino acid sequences

ncbi-tools-bin

6.1.20170106-2

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11

6.1.20170106-2

NCBI libraries for biology applications (X-based utilities)

paml

4.9g+dfsg-3

Phylogenetic Analysis by Maximum Likelihood (PAML)

parafly

0.0.2013.01.21-3build1

parallel command processing using OpenMP

phylip

1:3.696+dfsg-5

No description

phyml

3:3.3.20170530+dfsg-2

Phylogenetic estimation using Maximum Likelihood

picard-tools

2.8.1+dfsg-3

Command line tools to manipulate SAM and BAM files

primer3

2.4.0-1ubuntu2

Tool to design flanking oligo nucleotides for DNA amplification

pymol

1.8.4.0+dfsg-1build1

Molecular Graphics System

qiime

3:3.3.20170530+dfsg-2 (1.8.0+dfsg-4ubuntu1)?

Quantitative Insights Into Microbial Ecology

rasmol

2.7.5.2-2

Visualize biological macromolecules

raxml

8.2.11+dfsg-1

Randomized Axelerated Maximum Likelihood of phylogenetic trees

readseq

1-12

Conversion between sequence formats

rsem

1.2.31+dfsg-1

RNA-Seq by Expectation-Maximization

Rsubread

2.4.3

Mapping, quantification and variant analysis of sequencing data

samtools

1.7-1

processing sequence alignments in SAM and BAM formats

sift

4.0.3b-6

predicts if a substitution in a protein has a phenotypic effect

sortmerna

2.1-2

tool for filtering, mapping and OTU-picking NGS reads

stacks

2.0Beta8c+dfsg-1

pipeline for building loci from short-read sequences

sumatra

1.0.31-1

fast and exact comparison and clustering of sequences

swarm

2.2.2+dfsg-1

robust and fast clustering method for amplicon-based studies

t-coffee

2.2.2+dfsg-1 (11.00.8cbe486-6)

Multiple Sequence Alignment

tophat

2.1.1+dfsg1-1

fast splice junction mapper for RNA-Seq reads

transdecoder

5.0.1-1

find coding regions within transcripts

trinityrnaseq

2.5.1+dfsg-2