SlackBuilds

This is a list of what I maintain at SlackBuilds.org. The latest submission and updates can be viewed here. I am grateful for the help I received from the SlackBuilds community! If you have any comments, suggestions or just want to discuss some of the entries, please let me know.

Academic
CAFS_divergence | Clustering Analysis of Functional Shifts
CAPS_coevolution | Coevolution Analysis using Protein Sequences
Data2FCS | Data2FCS and FCS2Data
DendroPy | A Phylogenetic Computing Library
EMBASSY | EMBOSS associated software
EMBOSS | European Molecular Biology Open Software Suite
FCSalyzer | Flow cytometry analyser
FastTree | Infers approximately-ML phylogenetic trees
FigTree | A graphical viewer of phylogenetic trees
Gblocks | Select blocks of evolutionarily conserved sites
HMMER | Biosequence analysis using profile hidden Markov models
IGV | Integrative Genomics Viewer
MetaPhlAn2 | Metagenomic Phylogenetic Analysis
PhyML | Phylogenetic estimation using Maximum Likelihood
RAxML | Randomized Axelerated Maximum Likelihood
RepeatMasker | Screen DNA sequence for interspersed repeats
SeqMonk | A Mapped Sequence Analysis tool
TreeGraph | A feature rich phylogenetic tree editor
WEVOTE | WEighted VOting Taxonomic idEntification
aline | A Sequence Alignment Editor and Viewer
aliview | Alignment viewer and editor
amplicon | Design PCR primers on aligned sequences
amplifx | Manage, test and design your primers for PCR
archaeopteryx | Visualise, analyse and edit phylogenetic trees
arka | A GUI for genpak
bedGraphToBigWig | Convert bedGraph to bigWig file
bedtools | A powerful toolset for genome arithmetic
biopython | A set of Python tools for biological computation
bowtie | A short read aligner of DNA sequences
bowtie2-legacy | A tool for aligning sequencing reads
bpp-core | Bio++ Core Library
bpp-phyl | Bio++ Phyl Library
bpp-phyl-omics | Bio++ Phylogenetic Omics Library
bpp-popgen | Bio++ Population Genetics Library
bpp-seq | Bio++ Sequence library
bpp-seq-omics | Bio++ Sequence Omics Library
bpp1.9-numcalc | Bio++ 1.9 NumCalc Library
bpp1.9-phyl | Bio++ 1.9 Phyl Library
bpp1.9-seq | Bio++ 1.9 Seq Library
bpp1.9-utils | Bio++ 1.9 Utils Library
bppsuite | Bio++ program suite
bwa | Burrows-Wheeler Aligner
cap3 | DNA sequence assembly program
cistrome-CEAS | CEAS: Cis-regulatory Element Annotation System
cistrome-MACS | MACS: Model-based Analysis of ChIP-Seq
cistrome-conductGO | Find the top-n highest expressed TFs
cistrome-extra | Cistrome Applications Harvard extra apps
cistrome-mdseqpos | Cistrome Applications Harvard mdseqpos
clark-ugene | Ugene’s forked CLAssifier based on Reduced K-mers
clustalo | Clustal Omega
clustalw | Multiple Sequence Alignment
clustalx | Multiple Sequence Alignment GUI
cufflinks | A reference-guided assembler for RNA-Seq experiments
cutadapt | Trim adapters from high-throughput sequencing reads
datamash | Basic numeric, textual and statistical operations
diamond | A sequence aligner for protein and translated DNA
exonerate | A generic tool for sequence alignment
fiji | Fiji is just ImageJ
finchtv | A Brilliant Trace Viewer
gchemutils | gnome-chemistry-utils
gelemental | A periodic table viewer
geneconv | Statistical Tests for Detecting Gene Conversion
genometools | collection of bio-informatics tools
genpak | Utilities to manipulate DNA sequences
gp2fasta | Convert gp files to fasta
hyphy | Hypothesis Testing using Phylogenies
io_lib | Provides a trace file reading interface
iqtree | Efficient and versatile phylogenomic software by ML
isoelectric-point | Isoelectric point calculator
jalview | A Sequence Alignment Editor and Viewer
jellyfish_k-mer | A tool for counting of k-mers in DNA
kalign | A fast multiple sequence alignment program
kraken | Assign taxonomic labels to short DNA sequences
lalnview | Visualize local alignments
mafft | A multiple sequence alignment program
meme-db-gomo | MEME Suite GOMo databases
meme-db-motif | MEME Suite motif databases
meme-db-tgene | MEME Suite T-gene databases
meme-suite | Motif based sequence analysis tools
megax | Molecular Evolutionary Genetics Analysis
mkDSSP | A program that calculates DSSP entries from PDB entries
mrbayes | Bayesian Inference of Phylogeny
mumsa | A tool to assess MSA quality
muscle | A multiple sequence alignments program
muscle5 | MUSCLE 5: Next-generation MUSCLE
ncbi-blast | Basic Local Alignment Search Tool
ncbi-blast+ | BLAST+ CLI applications
ncbi-edirect | E-utilities on the Unix Command Line
ncbi-rmblastn | NCBI RMBlast
pal2nal | Create a codon-based DNA alignment
paml | PAML: Phylogenetic Analysis by Maximum Likelihood
pamlX | A GUI for PAML
perlprimer | Design primers for PCR and sequencing
plasmidomics | Plasmid Drawing Program
prank-msa | A probabilistic multiple alignment program
primer3 | Design PCR primers
samtools-legacy | Sequence Alignment/Map Tools version 0.1.19
seaview | Multiple sequence alignment and phylogeny GUI
seqkit | Ultrafast toolkit for FASTA/Q file manipulation
sequence-analysis | Biologic sequences analysis
sim | Local similarity program
snpEff | Genetic variant annotation and effect prediction toolbox
spades | SPAdes Genome Assembler
spidey | mRNA-to-genomic alignment
squizz | A sequence/alignment format checker and converter
staden | DNA sequence assembly, editing, and analysis tools
stringtie | Assembler of RNA-Seq alignments
t_coffee | A multiple sequence alignment program
tabix-legacy | Legacy version of Tabix
topdraw | A sketchpad for protein topology diagrams
tophat | Splice junction mapper for RNA-Seq reads
treebest-ensembl | Tree Building guidEd by Species Tree
treerecs | Treerecs: a tree reconciliation tool
treeviewx | Program to display phylogenetic trees
trimmomatic | A flexible read trimming tool for Illumina NGS data
trfind | Tandem repeats finder: a program to analyze DNA sequences
ucsc-blat | BLAT — The BLAST-Like Alignment Tool
ugene | A unified bioinformatics toolkit
vCAPS_coevolution | Coevolution Analysis using Protein Sequences
vcftools | A program package designed for working with VCF files
wehi-cellsymphony | Audio representation of flow cytometric data
wehi-deid | Flow cytometry De-Identifier
wehi-hackit | Clip a stream of cells from flow cytometry files
wehi-weasel | Flow cytometry data analysis and display program
wise | Compare protein to DNA sequence

Audio
pavucontrol-qt | Qt port of pavucontrol
rezound | audio file editor
xmms-wma | support for WMA V1/V2 in XMMS

Desktop
LX-Colors-Revival | GTK2/GTK3/Openbox themes
clearlooks-classic-themes | The classic Clearlooks themes
gtk1-industrial-engine | GTK1 engine and theme
gtk1-theme-switch | Theme chooser for GTK1
gnome-icon-theme | default icons used by GTK+
gnome-icon-theme-stock | Gnome 2 stock icons subset
gtk-xfce-engine | Xfce Gtk+ engines
murrine-themes | Themes of the Murrine family
polar-cursor-themes | A smooth and simple cursor set
protozoa-cursor-themes | Animated cursor Protozoa themes
thunar-sendto-clamtk | A clamtk plugin for Thunar
xmms-skins-almond | Almond skins for XMMS
xmms-skins-ater | Ater skins for XMMS
xmms-status-plugin | Provides a status docklet for XMMS
xfce4-cpufreq-plugin | cpu frequency plugin for xfce4
xfwm4-themes | themes for the Xfce window manager

Development
rstudio-desktop | R Statistical IDE

Games
njam | The most addictive free pacman-like game
homm3_shareware_data | Heroes of Might and Magic III Demo
quake3_shareware_data | Quake III shareware data

Graphics
fyre | A tool for producing computational artwork
gpaint | GNU Paint: a small-scale GTK2 painting program
inkscape-gtk2 | Open Source vector graphics editor
mtpaint | Mark Tyler’s Painting Program

Libraries
PDFlib-Lite | A library to generate PDF files
alglib | A library for numerical analysis and data processing
libcifpp | libcif++: manipulate mmCIF and PDB files
muParser | A math parser library
qt-assistant-compat | Qt Assistant compatibility
tamu_anova | Contains both single and two factor ANOVA
tslib | C library for filtering touchscreen events

Misc
bodr | Blue Obelisk Data Repository
chemical-mime-data | Support for various chemical MIME types

Office
evince-gtk2 | a simple gnome-based document viewer
gcalctool-gtk2 | a graphical UNIX calculator
evince-gtk2 | GNOME spreadsheet app
gbgoffice | Bgoffice dictionary frontend
osmo-gtk2 | Handy Personal Organizer
referencer | Organize documents or references
wps-office | an office productivity suite for Linux
wps-office-dicts | Spell check dictionaries for WPS Office

Perl
perl-HTML-Template | HTML::Template
perl-Text-Soundex | Text::Soundex

Python
xopen | A xopen function that can deal with compressed files

System
apple-emoji | Apple Color Emoji
apple-fonts-Garamond | Apple fonts Garamond
apple-fonts-NY | Apple New York fonts
apple-fonts-SF | Apple San Francisco fonts
clamtk | A frontend for ClamAV
file-roller-gtk2 | an archive manager for GNOME
gnome-pkgtool | A GTK+ front-end to pkgtool
ktsuss | keep the su simple, stupid
pbzx | pbzx stream parser