linux生物代谢图软件,Linux 系统下的生物信息软件The Linux for Biotechnology project|生物软件网...

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