This book is suitable for classroom use as a general introduction to programming concepts.

More at http://tldp.org/LDP/abs/html/

Address of the bookmark: http://tldp.org/LDP/abs/html/

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the GBrowse HOWTO During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required!) Later we will show how to set up a genome size database using the berkeleydb and MySQL adaptors.

More at http://elp.ucdavis.edu/tutorial/tutorial.html

Address of the bookmark: http://elp.ucdavis.edu/tutorial/tutorial.html

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

https://bioinformaticsworkbook.org/

Address of the bookmark: https://bioinformaticsworkbook.org/

ALF
A Simulation Framework for Genome Evolution
http://www.cbrg.ethz.ch/alf

Bayesian Serial SimCoal
Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider.
http://www.stanford.edu/group/hadlylab/ssc/index.html

BEERS
BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data
http://cbil.upenn.edu/beers/

BOTTLENECK
Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies
http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html

BottleSim
BottleSim is a computer simulation program for simulating the process of population bottlenecks
http://chkuo.name/software/bottlesim.html

CASS
Protein Sequence Simulation
http://www.wyomingbioinformatics.org/liberlesgroup/cass/

CDPOP
CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior.
http://cel.dbs.umt.edu/cdpop

CoalFace
CoalFace is a simulation of the coalescent process with the visual display of gene genealogies.
http://web.up.ac.za/default.asp?ipkcategoryid=3283

CoaSim
CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
http://users-birc.au.dk/mailund/coasim/index.html

cosi
The cosi package is written in C and is available as a tar file.
http://www.broadinstitute.org/~sfs/cosi/

CS-PSeq-Gen
A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny
http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen.html

DAWG
An application designed to simulate the evolution of recombinant DNA sequences in continuous time
http://scit.us/projects/dawg

Easypop
EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions
http://www.unil.ch/dee/page36926_fr.html

EggLib
EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
http://egglib.sourceforge.net/

EvolSimulator
A simulation test bed for hypotheses of genome evolution
http://acb.qfab.org/acb/evolsim/

EvolveAGene
A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions
http://bellinghamresearchinstitute.com/software/index.html

fastsimcoal
A continuous-¬‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
http://cmpg.unibe.ch/software/fastsimcoal/

FastSLINK
Simulation of Marker and Phenotype Data in Pedigrees
http://watson.hgen.pitt.edu/

FFPopSim
C++/Python library for population genetics.
http://webdav.tuebingen.mpg.de/ffpopsim/

FLUX SIMULATOR
The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters.
http://flux.sammeth.net/simulator.html

ForSim
ForSim: A Forward Evolutionary Computer Simulation
http://www.anthro.psu.edu/weiss_lab/research.shtml

ForwSim
The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process.
http://badri-populationgeneticsimulators.blogspot.com/

FPG
Forward Population Genetic simulation
http://genfaculty.rutgers.edu/hey/software#fpg

FREGENE
FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations.
http://www.ebi.ac.uk/projects/bargen/download/fregen/documentation_html.html

GAMETES
Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci.
http://sourceforge.net/projects/gametes/?source=navbar

GASP
Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models.
http://research.nhgri.nih.gov/gasp/

GemSIM
Next generation sequencing read simulator
http://sourceforge.net/projects/gemsim/

GeneArtisan
Simulation of Markers in Case-Control Study Designs
http://www.rannala.org/?page_id=241

GENOME
A rapid coalescent-based whole genome simulator
http://www.sph.umich.edu/csg/liang/genome/

GenomePop2
GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version.
http://webs.uvigo.es/acraaj/genomepop2.htm

GenomeSimla
GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested
http://chgr.mc.vanderbilt.edu/genomesimla/

GENS2
Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions.
https://sourceforge.net/projects/gensim/

GWAsimulator
A rapid whole genome simulation program
http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator

HAP-SAMPLE
An association simulator for candidate regions or genome scans
http://www.hapsample.org/

HAPGEN
A simulator for the simulation of case control datasets at SNP markers
https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

HapSim
A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients
http://cran.r-project.org/web/packages/hapsim/index.html

HAPSIMU
A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model
http://l.web.umkc.edu/liujian/

IBDsim
IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models.
http://raphael.leblois.free.fr/

indel-Seq-Gen
A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies
http://bioinfolab.unl.edu/~cstrope/isg/

Indelible
A powerful and flexible simulator of biological evolution
http://abacus.gene.ucl.ac.uk/software/indelible/

invertFREGENE
InvertFREGENE is a forward-in-time simulator of inversions in population genetic data
http://www.ebi.ac.uk/projects/bargen/

kernalPop
A spatially explicit population genetic simulation engine
http://cran.r-project.org/src/contrib/archive/kernelpop/

MaCS
Markovian Coalescent Simulator
http://www-hsc.usc.edu/~garykche/

Mason
A package for the simulation of nucleotide data.
http://www.seqan.de/projects/mason/

mbs
modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html

Mendel's Accountant
Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine
http://mendelsaccount.sourceforge.net/

MetaSim
A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets
http://ab.inf.uni-tuebingen.de/software/metasim/

mlcoalsim
Multilocus Coalescent Simulations
http://code.google.com/p/mlcoalsim-v1/

ms
The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
http://home.uchicago.edu/~rhudson1/source/mksamples.html

msHOT
The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
http://home.uchicago.edu/~rhudson1/

msms
A coalescent Simlation tool with selection.
http://www.mabs.at/ewing/msms/index.shtml

MySSP
A program for the simulation of DNA sequence evolution across a phylogenetic tree
http://www.rosenberglab.net/software.php

Nemo
A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework.
http://nemo2.sourceforge.net/

NetRecodon
Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography
http://code.google.com/p/netrecodon/

PEDAGOG
Software for simulating eco-evolutionary population dynamics
https://bcrc.bio.umass.edu/pedigreesoftware/node/5

phenosim
A tool to add phenotypes to simulated genotypes
http://evoplant.uni-hohenheim.de/doku.php?id=software:software

PhyloSim
An R package for the Monte Carlo simulation of sequence evolution
http://bit.ly/rlsim-git

pIRS
Profile-based Illumina pair-end reads simulator
https://code.google.com/p/pirs/

ProteinEvolver
Simulation of protein evolution along phylogenies under structure-based substitution models
http://code.google.com/p/proteinevolver/

QMSim
QTL and Marker Simulator
http://www.aps.uoguelph.ca/~msargol/qmsim/

quantiNEMO
An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population
http://www2.unil.ch/popgen/softwares/quantinemo/

RECOAL
Simulates new haplotype data from a reference population of haplotypes.
ftp://popgen.usc.edu/

Recodon
Coalescent simulation of coding DNA sequences with recombination, migration and demography
http://code.google.com/p/recodon/

rlsim
A package for simulating RNA-seq library preparation with parameter estimation
http://bit.ly/rlsim-git

Rmetasim
Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R
http://linum.cofc.edu/software.html#metasim

RNA Seq Simulator
RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets.
http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator

Rose
Random model of sequence evolution
http://bibiserv.techfak.uni-bielefeld.de/rose/

SelSim
SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection
http://www.well.ox.ac.uk/~spencer/selsim/

Seq-Gen
An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees.
http://tree.bio.ed.ac.uk/software/seqgen/

SEQPower
Statistical power analysis for sequence-based association studies
http://bioinformatics.org/spower/

SeqSIMLA
SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated.
http://seqsimla.sourceforge.net/

Serial NetEvolve
A flexible utility for generating serially-sampled sequences along a tree or recombinant network
http://biorg.cis.fiu.edu/sne/

SFS_CODE
SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.
http://sfscode.sourceforge.net/sfs_code/index/index.html

SIBSIM
Quantitative phenotype simulation in extended pedigrees
http://sourceforge.net/projects/sibsim/

SIMCOAL2
A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models
http://cmpg.unibe.ch/software/simcoal2/

SimCopy
An R package simulating the evolution of copy number profiles along a tree.
http://bit.ly/simcopy

SIMLA
SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies.
http://www.chg.duke.edu/research/simla.html

SimPed
A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures
http://www.hgsc.bcm.tmc.edu/content/simped

Simprot
A program to simulate protein evolution by substitution, insertion and deletion
http://www.uhnresearch.ca/labs/tillier/software.htm#3

SimRare
Rare variant simulation and analysis tool
http://code.google.com/p/simrare/

simuGWAS
A forward-time simulator that simulates realistic samples for genome-wide association studies.
http://simupop.sourceforge.net/cookbook/simucomplexdisease

simuPOP
simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.
http://simupop.sourceforge.net/

SISSI
A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.
http://www.cibiv.at/software/sissi/

SNPsim
Coalescent simulation of hotspot recombination
http://code.google.com/p/phylosoftware/

SPIP
SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user
http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434

Splatche
Spatial and Temporal Coalescences in Heterogeneous Environment
http://www.splatche.com/

srv
Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants.
http://simupop.sourceforge.net/cookbook/simurarevariants

SUP
SLINK/FastSLINK utility program
http://mlemire.freeshell.org/software.html

TreesimJ
A flexible, forward-time population genetic simulator
http://code.google.com/p/treesimj/

Vortex
VORTEX is an individual-based simulation model for population viability analysis (PVA).
http://www.vortex9.org/vortex.html

References:

Image www.evolution-of-life.com

www.cancer.gov

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

1. Duplication level
2. kmer profile
3. per base GC content
4. per base N content
5. per base quality
6. per base sequence content
7. per sequence GC content
8. per sequence quality
9. sequence length distribution

More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

• January 20th, 2016 - New! Bpipe 0.9.9 released!
• Download latest, all
• Documentation
• Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html