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The Linux for Biotechnology project (LfB)致力于收集各种Linux系统环境下的生物技术相关软件,并提供方便的点击安装操作及相关文献等等。原始网站
LFB计划的实施,使得生物学家可以用普通的PC机便可完成非常昂贵的服务器才能完成的工作。目前的LFB包括以下linux系统下的生物软件,资料加文献共计480M,解压后超过1G的内容,均加入到赠品光盘11,zp11中:

  • abacus - Analysis of Blake's Conjecture Using Simulations
  • ae2 - Sequence alignment editor
  • alfresco - Comparitive sequence analysis
  • artemis - DNA sequence viewer and annotation tool
  • beta - Estimation of alpha - Nonparametric linkage analysis
  • biomail - web-based application for medical researchers and biologists.
  • bioperl - perl tools for Molecular biology
  • biopython - Python tools for Molecular biology
  • codonW- A package for codon usage analysis.
  • DEODAS - DEgenerate Oligonucleotide Design & Analysis System
  • Distutils - Python distribution tools
  • DND - Protein molecular dynamics simulation/visualization
  • DomainFinder - An interactive program for the determination and characterization of dynamical domains in proteins.
  • dx - Data Explorer, visualisation package
  • e-PCR - Sequence mapping by Electronic PRC
  • EdIt - An automatic editor for DNA sequence data
  • efetch - Retrieve entries from sequence databases
  • EMBOSS - EMB Open Source Software
  • ESPript - Creates postrcipt sequence renderings
  • fastlink - Genetic linkage computations
  • garlic - Molecular visualization
  • GenoCheck - A method for detecting errors in pedigree data
  • genpak - Utilities to manipulate DNA sequences
  • gmaes - Evolution simulations
  • gperiodic - Periodic table
  • gibbs - Calculation of Probabilities for Diallelic Traits on Complex Pedigrees
  • hmmer - Biological sequence analysis using profile hidden Markov models
  • ImageJ - Java Image viewer
  • jalview - a java multiple alignment editor
  • jmol - an open-source molecule viewer and editor
  • kmol - Molecular weight calculator
  • ldb_2b - Hybrid mapping
  • LEKSBOT - a botanical lexicon
  • lintre - Phylogenetic tests of the molecular clock and linearized tree
  • melting - nearest-neighbor computation of nucleic acid hybridation
  • MIRA - DNA shotgun sequence data assembler
  • mmlib - A C++ macromolecular class library
  • mmtool - A macromolecular visualisation tool
  • pdbtool - A macromolecular visualisation tool
  • moldy - a general-purpose molecular dynamics simulation program
  • ncbi-tools - NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.
  • Blastall - NHGRI Blastall (a perl interface)
  • njbafd - Neighbor-joining tree construction from allele frequency data
  • njbtie - search all tie neighbor-joining trees and UPGMA trees and for bootstrapping
  • oligomap - OLIGOMAP is a tool to help researchers engineer restriction sites into oligonucleotides by silent mutagenesis
  • orfind - orfind is a command line version of ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html)
  • pdb2cif - convert PDB to CIF format
  • pftools - pftools is a collection of experimental programs supporting the generalized profile format and search method of PROSITE and NUCSITE.
  • pima - Pattern-Induced Multi-sequence Alignment program
  • pseudoknots - An extension of the Zuker M FOLD algorithm to optimal minimum energy prediction of pseudoknotted RNA structures
  • plato - Partial likelihoods expressed through optimisation
  • primer3 - Primer3 picks primers for PCR reactions
  • PSPP - Statistical analysis package.
  • puzzle - Maximum likelihood analysis for nucleotide, amino acid, and two-state data
  • PSeq-Gen - An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
  • QDate - Estimates date of divergence using data for sequence parirs
  • QuickPDB - Java Applet to view Protein Data Bank
  • rhmapper - A package for creating radiation hybrid maps
  • rnabob - searches for RNA motifs in sequence databases
  • SampLin - Data Acquisition package
  • sc_rate - Evaluates the quality of any sequence alignment.
  • Topal - Package for Detecting Recombination Breakpoints
  • RasMol2 - molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.
  • pasu - Probability and Statistics Utilities
  • PVM - Parallel Virtual Machine
  • PyMOL - molecular graphics program designed for rapid and efficient generation of high-quality molecular graphics animations.
  • seals - System for Easy Analysis of Lots of Sequences
  • sendbs - Average nucleotide diversity within and between populations
  • sequin - Program to aid submission of sequences to GenBank, EMBL and DDJB
  • seqsplit - Programs for running blastx on very long queries
  • sibs - Sib Pair Analysis
  • simPCR - check an sfind file from GCG for sequences that have homology to 2 opposite primers.
  • sog - algorithm to find the most parsimoneous nucleotide phylogenetic tree
  • TipDate - A program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences.
  • tRNAscan - a program for improved detection of transfer RNA genes in genomic sequence
  • treevolve - a program to simulate the evolution of DNA sequences under different population dynamic scenarios
  • vanilla - command line programs (written in Java) to provide simple access to the functionality of PAL
  • vaspview - scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package
  • w2h - WWW interface to the GCG Sequence Analysis Software Package
  • wise - DNA and protein sequence comparison package

所有以上软件均在RedHat (v6.2) 和SuSE (version 6.4)下测试通过。

以上软件,均加入到赠品光盘11,zp11中:

 

 

 

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