SlackBuilds

This is a list of what I maintain at SlackBuilds.org for the latest stable release of Slackware. The recent 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
EMBASSY | EMBOSS associated software
EMBOSS | European Molecular Biology Open Software Suite
FCSalyzer | Flow cytometry analyser
Gblocks | Select blocks of evolutionarily conserved sites
HMMER | Biosequence analysis using profile hidden Markov models
ImageJ | Image processing and analysis in Java
PhyML | Phylogenetic estimation using Maximum Likelihood
PhyTime | Phylogenetic estimation using Maximum Likelihood
QtiPlot | Data Analysis and Visualisation
aline | A Sequence Alignment Editor and Viewer
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
bowtie | A short read aligner of DNA sequences
bowtie2 | 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
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
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
exonerate | A generic tool for sequence alignment
fastqc | A quality control tool for high throughput sequence data
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
io_lib | Provides a trace file reading interface
ij-plugins-LOCI | LOCI Bio-Formats plugins for ImageJ
ij-plugins-UCSD | UCSD Confocal Microscopy Plugins for ImageJ
isoelectric-point | Isoelectric point calculator
jalview | A Sequence Alignment Editor and Viewer
lalnview | Visualize local alignments
mafft | A multiple sequence alignment program
megacc | Molecular Evolutionary Genetics Analysis
mkDSSP | A program that calculates DSSP entries from PDB entries
mrbayes | Bayesian Inference of Phylogeny
muscle | A multiple sequence alignments program
ncbi-blast | Basic Local Alignment Search Tool
ncbi-blast-plus | BLAST+ CLI applications
paml | PAML: Phylogenetic Analysis by Maximum Likelihood
pamlX | A GUI for PAML
perlprimer | Design primers for PCR and sequencing
plasmidomics | Plasmid Drawing Program
prarnk-msa | A probabilistic multiple alignment program
primer3 | Design PCR primers
samtools | Sequence Alignment/Map Tools
seaview | Multiple sequence alignment and phylogeny GUI
sequence-analysis | Biologic sequences analysis
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
t_coffee | A multiple sequence alignment program
tabix | Generic indexer for TAB-delimited genome position files
topdraw | A sketchpad for protein topology diagrams
tophat | Splice junction mapper for RNA-Seq reads
treeview | Program to display phylogenetic trees
ucsc-blat | BLAT — The BLAST-Like Alignment Tool
ugene | A unified bioinformatics toolkit
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
zotero | Collect, organize, cite, and share research sources

Audio
rezound | audio file editor
xmms-wma | support for WMA V1/V2 in XMMS

Desktop
clearlooks-classic-themes | The classic Clearlooks themes
gtk1-industrial-engine | GTK1 engine and theme
gtk1-theme-switch | Theme chooser for GTK1
murrine-themes | Themes of the Murrine family
polar-cursor-themes | A smooth and simple cursor set
protozoa-cursor-themes | Animated cursor Protozoa themes
slack-wallpapers | Slackware wallpapers
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

Games
digger | Digger remastered!
njam | The most addictive free pacman-like game
quake3_shareware_data | Quake III shareware data
vcmi | Engine for Heroes III: of Might and Magic
vcmi-core | VCMI core data files
vcmi-resolutions | Extra resolutions and bonus icons addon
vcmi-wog | Unofficial WoG addon

Graphics
fyre | A tool for producing computational artwork
gpaint | GNU Paint: a small-scale GTK2 painting program

Libraries
PDFlib-Lite | A library to generate PDF files
alglib | A library for numerical analysis and data processing
muParser | A math parser library
qt-assistant-compat | Qt Assistant compatibility
tamu_anova | Contains both single and two factor ANOVA

Misc
bodr | Blue Obelisk Data Repository
chemical-mime-data | Support for various chemical MIME types
igal2 | image gallery generator

Office
gbgoffice | Bgoffice dictionary frontend
referencer | Organize documents or references

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

System
clamtk | A frontend for ClamAV
ktsuss | keep the su simple, stupid



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