EgyptSearch Forums: Genetic Software Tools

...

»	EgyptSearch Forums » Egyptology » Genetic Software Tools

UBBFriend: Email this page to someone!

Author

Topic: Genetic Software Tools

xyyman
Member
Member # 13597

Rate Member

posted

Genetic Software Tools

https://www.nature.com/articles/nrg1904

for those interested

Computer programs for population genetics data analysis: a survival guide-Laurent Excoffier and Gerald Heckel

FURTHER INFORMATION
Berne’s CMPG (Computational and Molecular Population
Genetics) programs: http://cmpg.unibe.ch/software.htm
Bob Griffith’s GeneTree program:
http://www.stats.ox.ac.uk/~griff/software.html
Bruce Rannala’s programs:
http://www.rannala.org/labpages/software.html
Computational and Molecular Population Genetics
Laboratory homepage: http://cmpg.unibe.ch
Gil McVean’s programs:
http://www.stats.ox.ac.uk/~mcvean/
Giorgio Bertorelle’s programs:
http://web.unife.it/progetti/genetica/Giorgio/giorgio_soft.
html
Ian Wilson’s programs: http://www.mas.ncl.ac.uk/~nijw/
Jerôme Goudet’s programs:
http://www2.unil.ch/popgen/softwares/
Jinliang Wang’s programs:
http://www.zoo.cam.ac.uk/ioz/software.htm
Jody Hey’s programs:
http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm
Jonathan Pritchard’s programs:
http://pritch.bsd.uchicago.edu/software.html
Kent Holsinger’s programs:
http://darwin.eeb.uconn.edu/#software
Louis Bernatchez’s laboratory links and programs:
http://www.bio.ulaval.ca/louisbernatchez/links.htm#soft
Mark Beaumont’s programs:
http://www.rubic.rdg.ac.uk/~mab/software.html
Matthew Stephens’s programs:
http://www.stat.washington.edu/stephens/software.html
Montgomery Slakin’s programs:
http://ib.berkeley.edu/labs/slatkin/software.html
Montpellier’s CBGP (Centre de Biologie et de Gestion
des Populations) programs:
http://www.montpellier.inra.fr/URLB/
Montpellier’s Genome Populations Interactions Adaptation
laboratory’s programs:
http://www.genetix.univ-montp2.fr/index.htm#programmes
Noah Rosenberg’s programs:
http://rosenberglab.bioinformatics.med.umich.edu/
software.html
Oxford Evolutionary Biology Group’s programs:
http://evolve.zoo.ox.ac.uk/software.html
Oxford’s Mathematical Genetics programs:
http://www.stats.ox.ac.uk/mathgen/software.html
Peter Andolfatto’s programs:
http://www.biology.ucsd.edu/labs/andolfatto/programs/
programs.html
Rasmus Nielsen’s programs:
http://www.binf.ku.dk/~rasmus/webpage/programs.html
Richard Hudson’s programs:
http://home.uchicago.edu/~rhudson1/source.html
Ziheng Yang’s programs: http://abacus.gene.ucl.ac.uk/
Access to this links box is available online.

An Alphabetic List of Genetic Analysis Software . . . . . . . http://linkage.rockefeller.edu/soft/list1.html
Genetic Software Forum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . http://www.rannala.org/gsf
libsequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . http://molpopgen.org/software/libsequence_html/libsequence.htm
Nexus Class Library (version 2.0) . . . . . . . . . . . . . . . . . . . . . . . . . http://hydrodictyon.eeb.uconn.edu/ncl/
Population Genetics Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . http://www.geocities.com/CapeCanaveral/Lab/4709/popgen.htm
PyPop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . http://allele5.biol.berkeley.edu/pypop/index.html
Resources for Ecology, Evolutionary Biology,
Systematics, and Conservation Biology . . . . . . . . . . . . . . . . . http://darwin.eeb.uconn.edu/links/index.php
Software for Population Genetic Analyses . . . . . . . . . . . . . . http://www.biology.lsu.edu/general/software.html

Some freely downloadable computer programs and packages for analysing population genetics data, and related
programs and resources. See BOX 2 for links to additional resources.
Multi-purpose packages
Arlequin . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://cmpg.unibe.ch/software/arlequin3/
DnaSP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.ub.es/dnasp/
FSTAT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www2.unil.ch/popgen/softwares/fstat.htm
GDA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
Genepop . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://ftp.cefe.cnrs.fr/PC/MSDOS/GENEPOP
GENETIX . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.univ-montp2.fr/~genetix/genetix/genetix.htm
MEGA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.megasoftware.net/
MSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://i122server.vu-wien.ac.at/MSA/MSA_download.html
SPAGeDi . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.ulb.ac.be/sciences/ecoevol/spagedi.html
Individual-based programs
BayesAss+ . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.rannala.org/labpages/software.html
BAPS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.rni.helsinki.fi/~jic/bapspage.html
GeneClass. . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.montpellier.inra.fr/URLB/index.html
Geneland . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/Geneland.html
NewHybrids . . . . . . . . . . . . . . . . . . . . . . . .http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm
Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://pritch.bsd.uchicago.edu/software/structure2_1.html
Specialized programs
BATWING . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.mas.ncl.ac.uk/~nijw/
COLONISE . . . . . . . . . . . . . . . . . . . . . . . . . .http://www-leca.ujf-grenoble.fr/logiciels.htm
FDIST2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.rubic.rdg.ac.uk/~mab/software.html
Hickory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://darwin.eeb.uconn.edu/hickory/hickory.html
IM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM
LAMARC . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://evolution.gs.washington.edu/lamarc/lamarc_prog.html
Migrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://popgen.csit.fsu.edu/
MSVAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.rubic.rdg.ac.uk/~mab/software.html
Conversion programs
Convert. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.agriculture.purdue.edu/fnr/html/faculty/Rhodes/Students%20and%20Staff/
glaubitz/software.htm
Formatomatic . . . . . . . . . . . . . . . . . . . . . .http://taylor0.biology.ucla.edu/~manoukis/Pub_programs/Formatomatic/
XML specifications
BioPAX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.biopax.org/
MAGE-ML . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.mged.org/Workgroups/MAGE
SBML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://sbml.org/index.psp
R resources
HIERFSTAT . . . . . . . . . . . . . . . . . . . . . . . . . .http://www2.unil.ch/popgen/softwares/hierfstat.htm
R-project . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.r-project.org/
Statistical Genetics Resources . . .http://cran.au.r-project.org/src/contrib/Views/Genetics.html
Front-ends for command-line programs
CBSU . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://cbsuapps.tc.cornell.edu/index.aspx
Genepop on the web . . . . . . . . . . . . . .http://wbiomed.curtin.edu.au/genepop
SNAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.cals.ncsu.edu/plantpath/people/faculty/carbone/workbench.html
Individual programs not reviewed here
IMMANC . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.rannala.org/labpages/software.html
MESQUITE . . . . . . . . . . . . . . . . . . . . . . . . . .http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html
MR BAYES 3.1. . . . . . . . . . . . . . . . . . . . . . .http://mrbayes.csit.fsu.edu/
PHYLIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://evolution.genetics.washington.edu/phylip.html
STRUCTURAMA . . . . . . . . . . . . . . . . . . . .http://www.structurama.org/
TFPGA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .http://www.marksgeneticsoftware.net/tfpga.htm
HIERFSTAT, an R-package to compute and test hierarchical F-statistics; CBSU, Computational Biology

--------------------
Without data you are just another person with an opinion - Deming

Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007 | IP: Logged |

xyyman
Member
Member # 13597

Rate Member

posted

Introduction
POPBAM is a tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. The motivation for developing POPBAM is to provide the community with a fundamental suite of evolutionary analyses tools that would otherwise be tedious to implement. Since POPBAM works directly with BAM files, there are no intermediary steps necessary.

To enable POPBAM to perform population-level analyses, it is first necessary to modify the input BAM file header. Users must add the "PO" tag to the header line for each read group. The "PO" tag can be any string, as long as the string is identical between samples from the same population. One example may be that a BAM file has three read groups (R21, R22, and R25). The R22 and R25 read groups are from two different lines of Drosophila melanogaster called "MEL01" and "MEL02", while the third read group, R21, is from a single line of D. simulans called "SIM01". Below is an example of the BAM header including the "PO" tag:

--------------------
Without data you are just another person with an opinion - Deming

Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007 | IP: Logged |

Printer-friendly view of this topic