Biology and Slackware

This is a list of biology and chemistry oriented software, available at SlackBuilds.org. Relevant links to SBo are provided in [square brackets].

Suites

  • Bio++ Suite: is a package of programs using the Bio++ libraries and dedicated to Phylogenetics and Molecular Evolution. All programs are independent, but can be combined to perform rather complex analyses. [bpp-core] [bpp-phyl] [bpp-phyl-omics] [bpp-popgen] [bpp-seq] [bpp-seq-omics] [bppsuite]
  • EMBOSS: you will find hundreds of programs covering areas such as sequence alignment, database searching, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis, rapid identification of sequence patterns, presentation tools for publication. [EMBASSY] [EMBOSS]
  • Staden: the programs part of it (GAP4, GAP5, PREGAP4, SPIN and TREV) provide an excellent and fully developed set of DNA sequence assembly, editing, analysis and more. [io_lib] [staden]
  • Ugene: this integrates widely used bioinformatics tools within a common user interface. It provides visualization modules for biological objects such as: annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees, 3D structures. [ugene]

Versatile

  • Arka: Main scope of Arka is the manipulation and visualisation of DNA / RNA / protein sequences. [arka] [genpak]
  • Jalview: a free program developed for the interactive editing, analysis and visualization of MSA. It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures. [jalview]
  • SeaView: a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. [seaview]

PCR and sequencing

  • Amplicon: a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. [amplicon]
  • AmplifX: manage, test and design your primers for PCR. [amplifx]
  • Cutadapt: finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. [cutadapt]
  • Perlprimer: designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. [perlprimer]
  • Primer3: a widely used program for designing PCR primers. [primer3]
  • FastQC: aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. [fastqc]
  • FinchTV: a popular way to view DNA sequence traces. [finchtv]

Sequence alignment

  • ClustalW/X: a widely used, multiple sequence alignment program. [clustalx] [clustalw]
  • Clustal Omega: the latest addition to the Clustal family. It offers a significant increase in scalability and superior quality of alignments. [clustalo]
  • Mafft: a multiple sequence alignment program that offers a range of multiple alignment methods, L-INS-i, FFT-NS-2, etc. [mafft]
  • Muscle: a program for creating multiple alignments of amino acid or nucleotide sequences. [muscle]
  • T-coffee: it can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information, profile information or RNA secondary structures. [t_coffee]

 Sequence analysis

  • Aline: it can read common sequence alignment formats which the user can then alter, embellish, markup, etc to produce the kind of sequence figure commonly found in biochemical articles. [aline] [mkDSSP]
  • GP2FASTA: convert gp files from NCBI GenPept or GenBank to fasta format. Its main purpose is to create fasta files with short, but accurate headers for sequence. [gp2fasta]
  • Lalnview: a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). [lalnview]
  • IP: a small application to calculate the isoelectric point of a protein from its amino acid sequence. [isoelectric-point]
  • SA: a collage of coding projects for biologic sequences analysis. [sequence-analysis]
  • Squizz: a sequence/alignment format checker, but it has some conversion capabilities too. [squizz]

Homology searches

  • HMMER: used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). [HMMER]
  • NCBI-BLAST (plus): finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. [ncbi-blast] [ncbi-blast-plus]
  • UCSC-BLAT: a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments. [ucsc-blat]

Genome analysis

  • Bedtools: a swiss-army knife of tools for a wide-range of genomics analysis tasks. [bedtools]
  • Bowtie(2): an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. [bowtie] [bowtie2]
  • Bwa: an efficient program that aligns relatively short nucleotide sequences against a long reference sequence. [bwa]
  • Cap3: a DNA sequence assembly program, capable to clip 5′ and 3′ low-quality regions of reads, construct multiple sequence alignments of reads, and generate consensus sequences. [cap3]
  • Cistrome: this refers to “the set of cis-acting targets of a trans-acting factor on a genome-wide scale, also known as the in vivo genome-wide location of transcription factor binding-sites or histone modifications”. The term cistrome is a portmanteau of cistron + genome and was coined by investigators at the Dana-Farber Cancer Institute and Harvard Medical School. [cistrome-conductGO] [cistrome-extra] [cistrome-mdseqpos]
  • CEAS: a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. [cistrome-CEAS]
  • MACS: empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. [cistrome-MACS]
  • GenomeTools: a free collection of bio-informatics tools (in the realm of genome informatics) for biological sequence analysis and presentation. [genometools]
  • Geneconv: finds the most likely candidates for aligned gene conversion events between pairs of sequences in an alignment. [geneconv]
  • Samtools: provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. [samtools]
  • SnpEff: a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). [snpEff]
  • Spades: generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. [spades]
  • Spidey: a tool for aligning one or more mRNA sequences to a given genomic sequence. [spidey]
  • Tabix: a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. [tabix]
  • VCFtools: a program package designed for working with VCF files, aiming to provide validating, merging, comparing and calculate some basic population genetic statistics. [vcftools]

Transcriptome analysis

  • Cufflinks: assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. [cufflinks]
  • Tophat: a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes. [tophat]

Evolution

  • Archeopteryx: a tool for the visualization, analysis and editing of potentially large and highly annotated phylogenetic trees. [archeopteryx]
  • CAFS: simple and fast method for Clustering functionally divergent (FD) genes by Functional Category. [CAFS_divergence]
  • CAPS: aimed at measuring the coevolution between amino acid sites belonging to the same protein (intra-molecular coevolution) or to two functionally or physically interacting proteins (inter-molecular coevolution). [CAPS_coevolution]
  • Gblocks: eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. [Gblocks]
  • MrBayes: a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. [mrbayes]
  • PAML: a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. [paml] [pamlX]
  • PhyML: a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. [PhyML] [PhyTime]
  • TreeView: a simple program for displaying phylogenies. [treeview]

(Bio)Chemistry

  • gElemental: a periodic table viewer that provides detailed info on the chemical elements. [gelemental]
  • Ghemical: an easy-to-use molecular editor with OpenGL visualisation features and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common quantum chemistry codes. [ghemical]
  • GNOME Chemistry Utilities: a collection of libraries, programs and plugins that are useful for chemists and science students. [gchemutils]
  • Chemtool: a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11. [chemtool]
  • PyMOL: a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. [PyMOL]
  • wxMacMolPlt: a cross-platform GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. [wxmacmolplt]

Flow cytometry

  • FCSalyzer: a simple and free application for analysing flow cytometry data. It is based on the “What you see is what you get” principle with the hope of being intuitive to use. [FCSalyzer]
  • De-Identifier: Where flow cytometry data files from the clinic are to be used in research projects, DeID is used to remove patient identification. [wehi-deid]
  • Hackit: Where it is feared that a flow cytometry data file has been violated, for example at the start of the file by cells carried over from the previous sample, or at the end of the file by a nozzle blockage, Hackit can be used to clip the offending stream of cells from the file. [wehi-hackit]
  • WEASEL: a general purpose flow cytometry data analysis and display program developed at the Walter and Eliza Hall Institute of Medical Research (WEHI). Many different display formats are possible as are the extraction of a number of numerical or statistical measures. Multiple flow cytometry standard (FCS) data files can be compared side-by-side on screen and there is facility for fast scanning through collections of data files. Display layouts may be saved as may high quality graphics which may be incorporated into other documents. One of the program’s design parameters was to make operation as simple and intuitive as possible so self instruction should be the best course. [wehi-weasel]

Drawing and image processing

  • ImageJ: It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and “raw”. [ImageJ] [ij-plugins-LOCI] [ij-plugins-UCSD]
  • Plasmidomics: an open source program for easy drawing of plasmids and vector maps with high-quality graphics export. [plasmidomics]
  • Topdraw: sketchpad for drawing topology cartoons of proteins. It does not calculate topology from a PDB file, but
    merely allows you to sketch a topology derived from another source. [topdraw]

One response to “Biology and Slackware

  1. Pingback: Five years for Slackalaxy | slackalaxy

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