My Web Home
PICARD Homepage
Here I am not going to introduce how excellent and useful this toolset is, but to celebrate the the author finally integrate all tools into one package. So you will not need to find the package name every time you want it. Actually it’s boring to do that: set PICARDHOME or PICARD_HOME to the package root directory and find a package you want, and java –jar PACKAGE_NAME [options] ….
Now I am happy to to see all the functions are integrated into one package ‘picard.jar’. so you would just call
$> java –jar PICARDHOME/picard.jar
Here I am giving my way to install PICARDtools and use it simply.
Installation (Linux):
1. create a directory you want to install PICARDtools
$> mkdir -p $HOME/programs/picard/v1.124/x86_64
$> cd $HOME/programs/picard/v1.124/x86_64
2. Download the software from github
$> wget https://github.com/broadinstitute/picard/releases/download/1.124/picard-tools-1.124.zip
$> unzip picard-tools-1.124.zip
$> ls
picard-tools-1.124
$> mv picard-tools-1.124 bin
$> cd bin
$>ls -1
htsjdk-1.124.jar
libIntelDeflater.so
picard.jar
picard-lib.jar
3. [optional] create one link to directly call picard.jar
$> vim picard
#press i on your keyboard to enter VIM edit mode
#pasta following into terminal:
——————————-file border—do not copy this line——————————-
#!/bin/sh
CurDir=$(cd `dirname $(readlink -f $0)`; pwd)
java -jar $CurDir/picard.jar “$@”
——————————file border—–do not copy this line—————————–
#press Esc, and then input :wq to save and exit
#This is to create one file containing content described above. Same with other text editor, like gedit
$> chmod +x ./picard
#And then put this picard file into you PATH by editing ~/.bashrc, /etc/profile or other ways.
$> export PATH=$HOME/programs/picard/v1.124/x86_64/bin:$PATH
in my case, to make the setting immediately work. But remember to change the picardpath to yours.
4. test
$> picard
USAGE: PicardCommandLine <program name> [-h]
Available Programs:
————————————————————————————–
Fasta: Tools for manipulating FASTA, or related data.
CreateSequenceDictionary Creates a SAM or BAM file from reference sequence in fasta format
ExtractSequences Extracts intervals from a reference sequence, writing them to a FASTA file
NormalizeFasta Normalizes lines of sequence in a fasta file to be of the same length
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Illumina Tools: Tools for manipulating data specific to Illumina sequencers.
CheckIlluminaDirectory Asserts the validity of the data in the specified Illumina basecalling data
CollectIlluminaBasecallingMetrics Given an Illumina basecalling and a lane, produces per-lane-barcode basecalling metrics
CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given basecalling analysis directory
CollectIlluminaSummaryMetrics Collects summary metrics according to Illumina specifications.
ExtractIlluminaBarcodes Tool to determine the barcode for each read in an Illumina lane
IlluminaBasecallsToFastq Generate fastq file(s) from data in an Illumina basecalls output directory
IlluminaBasecallsToSam Generate a SAM or BAM file from data in an Illumina basecalls output directory
MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags
————————————————————————————–
Interval Tools: Tools for manipulating Picard interval lists.
BedToIntervalList Converts a BED file to an Picard Interval List.
IntervalListTools General tool for manipulating interval lists
LiftOverIntervalList Lifts over an interval list from one reference build to another
ScatterIntervalsByNs Writes an interval list based on splitting the reference by Ns
————————————————————————————–
Metrics: Tools for reporting metrics on various data types.
CalculateHsMetrics Calculates Hybrid Selection-specific metrics for a SAM or BAM file
CollectAlignmentSummaryMetrics Produces from a SAM or BAM a file containing summary alignment metrics
CollectBaseDistributionByCycle Program to chart the nucleotide distribution per cycle in a SAM or BAM file.
CollectGcBiasMetrics Collects information about GC bias in the reads in the provided SAM or BAM
CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
CollectInsertSizeMetrics Writes insert size distribution metrics for a SAM or BAM file
CollectJumpingLibraryMetrics Produces jumping library metrics for the provided SAM/BAMs
CollectMultipleMetrics A “meta-metrics” calculating program that produces multiple metrics for the provided SAM/BAM
CollectOxoGMetrics Collects metrics quantifying the CpCG -> CpCA error rate from the provided SAM/BAM
CollectQualityYieldMetrics Collects a set of metrics that quantify the quality and yield of sequence data from the provided SAM/BAM
CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file
CollectRrbsMetrics Collects metrics about bisulfite conversion for RRBS data
CollectTargetedPcrMetrics Produces Targeted PCR-related metrics given the provided SAM/BAM
CollectWgsMetrics Writes whole genome sequencing-related metrics for a SAM or BAM file
EstimateLibraryComplexity Estimates library complexity from the sequence of read pairs
MeanQualityByCycle Writes mean quality by cycle for a SAM or BAM file
QualityScoreDistribution Charts quality score distributions for a SAM or BAM file
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Miscellaneous Tools: A set of miscellaneous tools.
BaitDesigner Designs baits or oligos for hybrid selection reactions.
FifoBuffer FIFO buffer used to buffer input and output streams with a customizable buffer size
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SAM/BAM: Tools for manipulating SAM, BAM, or related data.
AddCommentsToBam Adds comments to the header of a BAM file
AddOrReplaceReadGroups Replaces read groups in a BAM or SAM file with a single new read group
BamIndexStats Generates index statistics from a BAM file
BamToBfq Create BFQ files from a BAM file for use by the Maq aligner.
BuildBamIndex Generates a BAM index (.bai) file
CalculateReadGroupChecksum Creates a hash code based on the read groups (RG) in the SAM or BAM header.
CheckTerminatorBlock Asserts the provided gzip file’s (e.g., BAM) last block is well-formed; RC 100 otherwise
CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
CompareSAMs Compares two input SAM or BAM files
DownsampleSam Down-sample a SAM or BAM file to retain a random subset of the reads
FastqToSam Converts a fastq file to an unaligned BAM or SAM file
FilterSamReads Creates a new SAM or BAM file by including or excluding aligned reads
FixMateInformation Ensure that all mate-pair information is in sync between each read and its mate pair
GatherBamFiles Concatenates one or more BAM files together as efficiently as possible
MarkDuplicates Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
MarkDuplicatesWithMateCigar Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
MergeBamAlignment Merges alignment data from a SAM or BAM with data in an unmapped BAM file
MergeSamFiles Merges multiple SAM or BAM files into one file
ReorderSam Reorders reads in a SAM or BAM file to match ordering in reference
ReplaceSamHeader Replace the SAMFileHeader in a SAM file with the given header
RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs
RevertSam Reverts SAM or BAM files to a previous state
SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM
SamToFastq Converts a SAM/BAM into a FASTQ
SortSam Sorts a SAM or BAM file
SplitSamByLibrary Splits a SAM or BAM file into individual files by library
ValidateSamFile Validates a SAM or BAM file
ViewSam Prints a SAM or BAM file to the screen
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VCF/BCF: Tools for manipulating VCF, BCF, or related data.
FilterVcf Hard filters a VCF.
GatherVcfs Gathers multiple VCF files from a scatter operation into a single VCF file
GenotypeConcordance Calculates the concordance between genotype data for two samples in two different VCFs
MakeSitesOnlyVcf Creates a VCF bereft of genotype information from an input VCF or BCF
MergeVcfs Merges multiple VCF or BCF files into one VCF file or BCF
RenameSampleInVcf Rename a sample within a VCF or BCF.
SortVcf Sorts one or more VCF files
SplitVcfs Splits an input VCF or BCF file into two VCF or BCF files
UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
VcfFormatConverter Converts a VCF file to a BCF file, or BCF to VCF
VcfToIntervalList Converts a VCF or BCF file to a Picard Interval List.
————————————————————————————–
#To use subfunctions: just call that behind picard, like:
$> picard SamToFastq
#To see options help of SamToFastq
……
WORKS. DONE. I am genius…… Ho………HighFive…….
Leave a comment if you think it’s helpful please.
[Another much larger list is at: http://www.nslij-genetics.org/soft/ Seems to contain many programs that are not of intense interest to those whose primary interest is population genetics of natural populations…]
Program list
AFLPOP 1.1.xls –see Duchesne
AFLP-SURV – see Vekemans
API-CALC see Ayres
Arlequin — see Excoffier
Assignment tests — see Paetkau, also Cornuet.
Beast – see Drummond
BLAST — NIH site for finding related DNA sequences http://www.ncbi.nlm.nih.gov/BLAST/
Bottleneck — — see Cornuet
CAIC –- see Purvis
Cervus — see Marshall
ClustalX — sequence alignment software
http://inn-prot.weizmann.ac.il/software/ClustalX.html (Mac, Windows, Linux et al.)
CPC — see Phillips Common Principal Components
Delrious (relatedness Mathematica notebook)– see Stone
DISPAN – see http://mep.bio.psu.edu/readme.html
distruct – see Rosenberg
Excel Microsatellite Toolkit — Park
famoz Mol Ecol Notes online Aug-03
FSTAT — see Goudet
GDA — see Lewis
GENALEX – see Peakall
GENECLASS — see Cornuet
GENEPOP — see Raymond and Rousset
GeneStat — see Lewis.
Genetix — see Montpelier .
Genographer – see Benham, James MSU
GeoDis — see Posada
Gimlet – see Valière
Hickory – see Holsinger
Identix (Français)— see Belkhir
IMMANC — see Rannala.
Kinship — see Goodnight and Queller.
LEA — see Langella
MARK – see Ritland
McMantell — see McDonald.
MEGA — see Kumar
Micsat — see Wilson.
Microsat — see Stanford (Goldstein, Shriver et al.)
Migrate — see Beerli.
MISAT — see Nielsen.
MS Tools (Excel macro utility)– see Park
MSA (microsatellite analyzer) — see Schlotterer
Parentage — see Emery et al.
Partition — see Dawson and Belkhir Bayesian approach
PartitionML — see Belkhir
PCAGen — see Goudet.
PDAP – see Garland
PHYLIP — see Felsenstein.
POPGENE – see
Populations — see Langella
PowerSSR — see Liu
Relatedness 5.07— see Goodnight and Queller.
RSTCalc— see Goodman (Goudet’s FSTAT also)
Sample size calculator — see York Univ. stats web
SPAGeDi — see Hardy
Structure — see Pritchard
SWEEP_BOTT (requires C) – see Galtier
TextWrangler – utility converts Mac OSX carriage returns to Unix line feeds; see Felsenstein.
TFPGA — see Miller.
TreeExplorer — see Kumar
TreeView — see Page.
WINAMOVA — see Michalakis and Excoffier.
Measures produced:
Alignment of DNA sequences: ClustalX
Allelic richness: FSTAT
Cavalli-Sforza distances: PHYLIP, TFPGA (?)
Dominant marker analyses: AFLPOP, AFLP-Survey, Hickory
F-statistics: FSTAT, GDA, GenePop, GeneStat, Genetix.
Gene diversity (D): GeneStat, TFPGA, Genetix.
Gene frequencies: (from genotypic data) FSTAT, Relatedness, others.
GST: GeneStat, FSTAT, TFPGA.
Hardy-Weinberg fit: GenePop, FSTAT, TFPGA, Arlequin.
Independent contrasts CAIC
K (number of pops.) Structure
Mantel tests: Genetix, TFPGA, McMantell.
Ne (effective pop. size): Migrate, Misat.
Nei’s distance(’72, ’78): AFLP-Survey, GeneStat, GDA, FSTAT, TFPGA
(PHYLIP Nei’s 1972 only).
Nei and Li (1979) RestDist in PHYLIP (useful for individual-based trees with
AFLP data)
Nested clade GeoDis
PCA: Principal comp. Analysis w/ PCP, PCAGen, MiniTab
Phylo-independent contrast CAIC, PDAP
Relatedness Relatedness, Identix, SPAGeDi, delrious, MARK, AFLP-Surv
RST: FSTAT, Genetix, RSTCalc.
Rogers’ distance: TFPGA, GeneStat.
Theta (Q): GDA, FSTAT. (Cockerham & Weir F-stat)
Tree diagrams: TreeView
Q (F-statistic): PowerSSR, GDA, FSTAT, Genetix. (Cockerham & Weir)
Q = 4 Neµ Migrate, Misat
Alphabetical, by author/programmer.
________________________________________________________________
Ayres, K.L. and A.D.J. Overall. 2004. API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol. Ecol. Notes 4: 315-318.
http://www.rdg.ac.uk/statistics/genetics/
API-CALC v. 1.0 Windows 19-Nov-04
Calculates the probability of identification in the presence of given degrees of relatedness in the population, inbreeding and coancestry
________________________________________________________________
http://popgen.csit.fsu.edu/ miggui 0.8 Graphical interface for Mac OSX10.2+
http://evolution.genetics.washington.edu/lamarc/migrate.html
Migrate Version 2.0.6 26-May-05 √ Macintosh
Requires repeat numbers for input if using SMM. Takes huge amount of time (days)
Beerli, P. 1998. Estimation of migration rates and population sizes in geographically structured populations. Pp. 39-53In Advances in molecular ecology (G. Carvalho, ed.). NATO-ASI workshop series. IOS Press, Amsterdam.
Beerli, P. and J. Felsenstein. 1999. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773.
________________________________________________________________
Belkhir, K., Castric, V., and F. Bonhomme. 2002. IDENTIX, a software to test for relatedness in a population using permutation methods.
Identix
http://www.univ-montp2.fr/~genetix/labo.htm#programmes (actual download)
http://www.univ-montp2.fr/%7Egenetix/identix_ms.pdf (downloads PDF)
Site is clunky and download is unclear, but…..
See “Identix.pdf” Input can be “Import” of GenePop inputs created in MS Tools
(mise en garde, on doit comprendre un peu de Français; logiciels means software, téléchargement means download – bonne chance)
Partition ML http://www.univ-montp2.fr/%7Egenetix/partitionml.htm
ftp://162.38.181.25/pub/partitionml.zip (actual download)
________________________________________________________________
Benham, James. MT State U. (Hordeum Sequencer User group) james_benham@hmc.edu
Genographer 1.6. Java 11-Sep-04 √
This program will read in data from an ABI 3700, 3100, 377 or 373, CEQ 2000 or SCF and reconstruct them into a gel image which is straightened and sized. Bins can be defined easily and viewed as thumbnails, which allows for a fairly quick and easy way of scoring a gel.
http://hordeum.oscs.montana.edu/genographer/
________________________________________________________________
Cornuet, J.-M.
http://www.montpellier.inra.fr/URLB/geneclass/geneclass.html
GENECLASS 1.0.02 Windows 26-Oct-04 √
GeneClass is a program for assignation and exclusion using molecular markers
(similar to, but more diverse than Paetkau assignment testing; includes Bayesian approach)
Has not been updated since 1999
http://www.ensam.inra.fr/URLB/bottleneck/ bottleneck.html
BOTTLENECK 1.2.02 Windows 28-Aug-01 √
Uses GENEPOP input format
Detecting recent effective population size reductions from allele data frequencies
From URLB/ Pop100gene is a small tool for population genetics that compute various informations.
________________________________________________________________
Dawson, K.J., and K. Belkhir. A Bayesian approach to the identification of panmictic populations and the assignment of individuals. 2001. Genetical Research 78: 59-77.
http://www.genetix.univ-montp2.fr/partition/partition.htm
Improved link for Partition Windows 20-Oct-02 Uses same inputy format as Genetix
(on doit comprendre un peu de Français; logiciels means software, téléchargement means download – bonne chance)
PartitionML under Belkhir is a maximum likelihood approach
________________________________________________________________
DeWoody, U. of Georgia (Avise lab.) now at Purdue dewoody@fnr.purdue.edu
Parentage and exclusion programs. Matlab and Excel.
http://www.genetics.uga.edu/popgen/parentage.html
________________________________________________________________
Drummond, Alexei and Andrew Rambaut , University of Oxford
BEAST v1.0.3 2002-2003 Bayesian Evolutionary Analysis Sampling Trees
Windows, Mac, Linux (uses Java virtual machine) Aug-03 √
package for evolutionary inference from molecular sequences
BEAST uses a complex and powerful input format (specified in XML) to describe the evolutionary model. This has advantages in terms of flexibility in that the developers of BEAST do not have to try and predict every analysis that researchers may wish to perform and explicitly provide an option for doing it. However, this flexibility means it is possible to construct models that don’t perform well under the Markov chain Monte Carlo (MCMC) inference framework used. We cannot test every possible model that can be used in BEAST. There are two solutions to this: Firstly, we supply a range of recipes for commonly performed analyses that we know should work in BEAST and provide example input files for these (although, the actual data can also produce unexpected behaviour). Secondly, we provide advice and tools for the diagnosis of problems and suggestions on how to fix them:
http://evolve.zoo.ox.ac.uk/Beast/
________________________________________________________________
Duchesne, P., and L. Bernatchez. 2002. AFLPOP : A computer program for simulated and real population allocation based on AFLP data. Molecular Ecology Notes. 3: 380-383.
Assignment and other utilities for AFLP data.
http://www.bio.ulaval.ca/louisbernatchez/downloads.htm
AFLPOP Excel (with macros) 11-Sep-04 √
________________________________________________________________
Emery, A.M., I.J. Wilson, S. Craig, P.R. Boyle and R. Noble. 2001. Assignment of paternity groups without access to parental genotypes: multiple mating and development plasticity in squid. Molecular Ecology: 10: 1265-1278.
http://maths.abdn.ac.uk/~ijw/downloads/download.htm
Parentage Windows, Unix 20-Oct-02 √ PDF help file “parentage.pdf”
________________________________________________________________
http://anthropologie.unige.ch/arlequin/
Arlequin 2.000 Windows, Macintosh, Java 2-Nov-00 √
Does many kinds of analyses for many kinds of molecular data (RFLPs, AFLPs, minisatellites, sequences, microsatellites, allozymes et al.) Very difficult to get input correct. May work better via MSTools intermediary
________________________________________________________________
Felsenstein, Joe, U of Washington
http://evolution.genetics.washington.edu/
PHYLIP (many systematics, tree-building and pop. gen. routines)
Windows, PowerMac, C etc. For nice tree diagram program from PHYLIP treefile outputs see TreeView by Page.
Cite by: Felsenstein, J. 1995. PHYLIP (phylogeny inference package), version 3.57 manual. U. of Washington, Seattle.
[Infile notes: If you use PHYLIP on OSX you will likely find that you get an infile memory error due to carriage return issues (ASCII/ISO . I use a Mathematica routine, but you may want to download the free TextWrangler utility from http://www.barebones.com/products/textwrangler/download.shtml
Open the file in TextWrangler and click the 5th icon in the menu bar (the little page symbol) and then click Unix. Save and quit. File will now be acceptable to PHYLIP. You can also “Save as” MS-DOS with line breaks EACH TIME you modify the file. ]
LAMARC (Kuhner, Yamato, Beerli)
________________________________________________________________
Galtier, Nicolas, U Montpelier, France
http://biology.ucr.edu/people/faculty/Garland/PDAP.html
SWEEP_BOTT √ ANSI C (just learn C et un peu de Français over a weekend, and you’re on your way….)
dedicated to the detection of bottlenecks and selective-sweeps from a coalescence-based maximum-likelihood analysis of DNA sequence polymorphism data
Galtier N., Depaulis F., and Barton N.H. 2000. Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155: 981-987.
__________________________________________
http://biology.ucr.edu/people/faculty/Garland/PDAP.html
PDAP √ For Windows/DOS
PHENOTYPIC DIVERSITY ANALYSIS PROGRAMS; Independent contrasts etc.
Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292.
________________________________________________________________
Goodknight, K. & Queller
http://www.bioc.rice.edu/Keck2.0/labs/
Relatedness 5.07 √ For PowerMac (resolves problem with System 8.5)
Kinship 1.3 √ 2-Nov-00
Queller, D.C., and Goodnight, K.F. 1989. Estimating relatedness using genetic markers. Evol. 43, 258-275.
________________________________________________________________
http://helios.bto.ed.ac.uk/evolgen/rst/rst.html
RST Calc 2.2 Windows 25-Nov-99 √
Cite by: Goodman, S.J. 1997. RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and a determining their significance. Mol. Ecol. 6: 881-885.
________________________________________________________________
Goudet: (see also Raymond & Rousset GENEPOP) Lausanne University, Switzerland
Cite by: Goudet J. 1995. FSTAT Version 1.2: a computer program to calculate F-statistics.
J. Heredity 86: 485-486.
FSTAT Version 2.9.3.2 Windows 11-Sep-01 √ Nov-04
http://www2.unil.ch/popgen/softwares/fstat.htm
Assesses several variance-based measures (Theta Q of Weir and Cockerham),
RST of Goodman, allelic richness. Tests for HWE, various other things.
PCAGEN Windows Principal components analysis of gene frequency data.
http://www2.unil.ch/popgen/softwares/pcagen.htm 28-Nov-99 √
________________________________________________________________
http://www.ulb.ac.be/sciences/lagev/spagedi.html
SPAGeDi Version 1.2d Windows 30-Aug-04√
Computes various statistics describing relatedness or differentiation between individuals or populations by pairwise comparisons, and analyze how these values are related to geographical distances, 1°) in a way similar to a spatial autocorrelation analysis, 2°) by linear regressions (the slopes of these regressions can be used to obtain indirect estimates of gene dispersal distances parameters such as neighborhood size). The statistics computed include Fst, Rst, Ds (Nei’s standard genetic distance), and (delta mu)2 (Goldstein and Pollok 1997) for analyses at the population level and, for analyses at the individual level, pairwise kinship, relatedness and fraternity coefficients as well as Rousset’s distance between individuals and a kinship analogue based on allele size. Jackknife over loci gives approximate standard errors, and permutations of locations, individuals or genes provide ad hoc tests. In addition, the actual variance of these statistics can be estimated following the method of Ritland (2000), providing a measure necessary for marker-based inference of the heritability or Qst of quantitative traits.
________________________________________________________________
Holsinger, Kent, and Paul Lewis, U. of Conn.
http://darwin.eeb.uconn.edu/hickory/hickory.html
Hickory V. 1.03 Windows 1-Jun-05√
The software implements the Bayesian method described in Holsinger (1999) for estimating F-statistics co-dominant marker data and the method described in Holsinger et al. (2002) for estimating F-statistics from dominant marker data. It also includes routines to allow posterior comparisons as described in Holsinger and Wallace (2004).
Holsinger, K. E. 1999. Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130:245–255.
Holsinger, K. E., and L. E. Wallace. 2004. Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology 13:887-894.
Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11:1157-1164.
________________________________________________________________
Kumar, S.: (Authors: Sudhir Kumar, Koichiro Tamura, Ingrid Jakobsen, Masatoshi Nei)
http://www.megasoftware.net/
MEGA v. 4.0 ß Version Windows 7-Apr-07 √
“…the goal of the MEGA (Molecular Evolutionary Genetics Analysis) software project has been to make useful methods of comparative sequence analysis easily accessible to the scientific community
TreeExplorer (embedded in MEGA) has a great feature that allows one to collapse branches in individual-based trees to show homogeneous clades
Nei, M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford Univ. Press, NY. ISBN 0195135857
________________________________________________________________
Langella, O Olivier.Langella@pge.cnrs-gif.fr
http://www.pge.cnrs-gif.fr/bioinfo/wini386/populations.exe
http://www.pge.cnrs-gif.fr/bioinfo/ (then look at [cryptic] list of software choices in banner near top of screen; pour d’autres on doit comprendre un peu de Français; logiciels means software)
Populations 1.2.24 Apr-02 Windows . Population genetic software (individuals or populations distances, phylogenetic trees).
http://www.pge.cnrs-gif.fr/bioinfo/lea/index.php?lang=en
LEA Likelihood based estimation of admixtures.
Langella O., L. Chikhi, and M. Beaumont. 2001 LEA (Likelihood-based estimation of admixture) : a program to simultaneously estimate admixture and the time since admixture Molecular Ecology Notes 1(4): 357-358.
(on doit comprendre un peu de Français; logiciels means software, téléchargement means download – bonne chance)
________________________________________________________________
http://lewis.eeb.uconn.edu/lewishome/software.html
GDA v. 1.0d13 Windows 28-Aug-01 √. Calculates many of the genetic estimates found in Weir, B.S. 1996. Genetic Data Analysis. Sinauer, Sunderland, MA.
GeneStat. Old DOS-based program for analysis of codominant, allelic marker data. D. McD. has this on diskette and computers.
Cite by: Lewis, P. O., and R. Whitkus. 1989. GENESTAT for microcomputers. ASPT Newsletter 2: 15-16.
________________________________________________________________
http://www.stat.ncsu.edu/~kliu2/index.htm
PowerSSR Windows 8-Apr-02 √. PowerSSR is a comprehensive set of statistical methods for discrete genetic data analysis, designed especially for microsatellite data analysis. From the NC State Weir lab. (Website not active Oct-02)
________________________________________________________________
http://helios.bto.ed.ac.uk/evolgen/cervus/cervusregister.html
CERVUS 1.0 Windows 25-Nov-99
Cite by: Marshall, TC, Slate, J, Kruuk, L and Pemberton, JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7: 639-655.
________________________________________________________________
McDonald, D.B.. University of Wyoming
McDonald, D.B., W.K. Potts, J.W. Fitzpatrick, and G.E. Woolfenden. 1999. Contrasting genetic structures in sister species of North American scrub-jays. Proc. Royal Soc. London B. 266: 1117-1125.
dbmcd@uwyo.edu
McMantell — Macintosh (System 9/Classic) application that conducts a Mantel test (correspondence between genetic and geographic distances). A separate randomization procedure compares strength of correlation across two sets of matrices. That is, in addition to asking whether genetic distance correlates with geographic distance, one can ask whether the correlations in data set one are stronger than those in set two.
Also available as a Mathematica notebook by request to McD, (requires expensive Mathematica software, so worth it only if you already use Mathematica: http://www.wolfram.com/)
________________________________________________________________
http://acasun1.unige.ch/LGB/Software/Windoze/amova
WINAMOVA
or ftp from acasun1.unige.ch/pub/comp/win/amova
________________________________________________________________
Miller, Mark P. Tools for Population Genetic Analyses TFPGA ASU post-doc
Mark.Miller@cnr.usu.edu
20-Nov-01 √
Includes Mantel test , AMOVA Prep Major overlap with other programs
________________________________________________________________
Montpelier group Genetix 4.05 Belkhir K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme
http://www.univ-montp2.fr/~genetix/genetix/genetix.htm
20-Jun-06 √
Includes F-statistics, permutation tests for HWE, Mantel (on doit comprendre un peu de Français; logiciels means software, téléchargement means download – bonne chance)
See also Partition, which uses same data input format
Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F. 1996-2002 GENETIX 4.04, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France).
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NCSU Power SSR Windows program for microsatellite analysis
http://www.stat.ncsu.edu/~kliu2/download.htm
28-Feb-02 √
17 distance measures, 4 hierarchy levels
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Nielsen, Rasmus
http://www.biom.cornell.edu/Homepages/Rasmus_Nielsen/misat/misat.1.0.exe
http://ib.berkeley.edu/labs/slatkin/rasmus/MISAT.1.0.hqx
Misat 1.0 for PowerMac or (newer) Windows October-01 √
Calculates 4Nµ. See McD. ln-regression approach to resolving multi-locus, multi-pop. output.
Nielsen, Rasmus. 1997. A likelihood approach to population samples of microsatellite alleles. Genetics 146: 711-716
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http://www.biology.ualberta.ca/jbrzusto/Doh.html
Assignment testing on the web Uses Titterington et al. 1981 for correction (ref in Msat refs. doc)
Based on Paetkau et al. 1995. Mol. Ecol. 4: 347 (Msat refs.doc)
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http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
TreeView (1.6.6 Sep-01). A nice application for producing images of trees. Works especially well from treefiles generated by PHYLIP. Windows, Macintosh.
OS X version (0.2.0) available Apr-02
Cite by: Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.
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Park, Stephen. Animal Genomics Lab, University College, Dublin, Ireland
spark@ucd.ie;
http://animalgenomics.ucd.ie/sdepark/ms-toolkit/
Excel Microsatellite Toolkit v. 3.1 Windows (only) Dec-01
An Excel spreadsheet toolkit for data conversion etc. The tools available allow you to check data, format data for population genetics programs (Arlequin, Microsat, Genepop, Fstat etc) and perform a number of basic calculations. The updated version allows you to:
work with haploid data as well as diploid data
save input files for genetics programs direct from Excel with no need for further editing
access help using the new help file
choose which loci and populations in your dataset to work with
calculate allele-sharing index of Chakraborty and Jin. 1993.
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Peakall, R., and Smouse, P. E. (2001) GenAlEx V5: Genetic Analysis in Excel. Population genetic software for teaching and research. Australian National University, Canberra, Australia..
http://www.anu.edu.au/BoZo/GenAlEx/
Excel-based package for teaching and analysis for a range of markers and problems.
Mac or Windows versions 8-Nov-04 √
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Phillips, P.C., and S.J. Arnold. 1999. Hierarchical comparison of genetic variance-covariance matrices. I. Using the Flury hierarchy. Evol. 53: 1506-1515.
http://www.uoregon.edu/~pphil/programs/cpc/cpc.htm
CPC – Common Principal Component Analysis Program
Mac Linux, DEC or Windows versions 20-Oct-02 √
Reference: Flury, B. 1988. Common Principal Components and Related Multivariate Methods. Wiley, New York
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http://bioag.byu.edu/zoology/crandall_lab/programs.htm
GeoDis: nested clade analyses of Templeton. Mol. Ecol. 9: 487-488.
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Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
Falush, D., M. Stephens, and J.K. Pritchard. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 7: 574–578.
http://pritch.bsd.uchicago.edu/ Windows 27-Jul-04 √
(V. 2.2 incorporates explicit accommodation of AFLP/domonant marker data. Since the manual is impenetrable for Mac installation and for file input format, I have put some tips below).
PDF of ms. as well as help file “Struct ReadMe.pdf” and “Pritchard.pdf”. Best not to give population information to Structure a priori.
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Purvis, A. Imperial College, UK
http://www.bio.ic.ac.uk/evolve/software/caic/ v. 2.6.9 Mar-02 Macintosh 18-Oct-05 √
Conducts comparative analysis by independent contrasts.
Purvis, A., and A. Rambaut (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Applications in the Biosciences (CABIOS) 11: 247-251.
Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125: 1-15.
Pagel, M.D. 1992. A method for the analysis of comparative data. J. theor. Biol. 156: 431-442.
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Rannala, Bruce. SUNY-Stony Brook
http://allele.bio.sunysb.edu/software.html
All the programs below are for Windows 95/NT
BMDC MLE of allele age Version 2.1 25-Nov-99 √
Slatkin, M., and B. Rannala. 1997. Estimating the age of alleles by use of intraallelic variability. Am. J. Human Genetics 60: 447-458.
PMLE estimation of gene flow Version 2.0 25-Nov-99 √
Rannala, B., and J. A. Hartigan. 1996. Estimating gene flow in island populations. Genetical Res. 67:147-158.
IMMANC Version 5.0 Nov-25-99 √ Joanna Mountain.
Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using multilocus genotypes. PNAS USA 94: 9197-9201.
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Raymond M. & Rousset F, 1995. GENEPOP (version 3.3): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249
Hardy-Weinberg test, differentiation, linkage disequilibrium
Very clunky DOS-based format!!!
ftp://ftp.cefe.cnrs-mop.fr/pub/pc/msdos/genepop
GENEPOP 3.1d Windows 28-Aug-01 √
Includes tests from the following references.
Garnier-Gere P and Dillmann C, 1992. A computer program for testing pairwise linkage disequilibria in subdivided populations. J Heredity 83:239.
Goudet J, Raymond M, De Meeüs T and Rousset F, 1996. Testing differentiation in diploid populations. Genetics 144:1933-1940.
Raymond M and Rousset F, 1995. An exact test for population differentiation. Evolution 49 :1280-1283.
Rousset F and Raymond M, 1995. Testing heterozygote excess and deficiency. Genetics 140 :1413-1419.
Rousset F, 1996. Equilibrium values of measure of population subdivision for stepwise mutation processes. Genetics 142 :1357-1362.
Rousset F, 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 : 1219-1228.
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Ritland, K. Multilocus estimation of pairwise relatedness with dominant markers. Mol. Ecol. 14: 3157-3165.
Assesses relatedness for dominant markers such as AFLP
http://www.genetics.forestry.ubc.ca/ritland/programs.html (not the same as listed in the paper!)
MARK (updated Sep-04) Windows 1-Oct-05 √
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Rosenberg, Noah noahr@usc.edu
http://www.cmb.usc.edu/people/noahr/distruct.html 26-May-05
Sun, Linux, Windows
distruct is a program that can be used to graphically display results produced by the genetic clustering program structure. The figures produced by distruct display individual membership coefficients in the same form as used in Genetic structure of human populations Science 298:2381-2385 (2002). Various options enable the user to control left-to-right printing order of populations, bottom-to-top printing order of clusters, colors, and other graphical details.
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Stanford (Lynch, Goldstein, Shriver)
http://hpgl.stanford.edu/projects/microsat/ 27-Nov-02
Microsat 1.5b software does many microsatellite distance analyses (e.g., dm2 of Goldstein, but may have errors e.g., in DSW of Shriver et al.) Macintosh
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http://i122server.vu-wien.ac.at/MSA/MSA_download.html 11-Oct-04
Microsatellite Analyzer software does many microsatellite distance analyses Macintosh or Windows
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Delrious is a computer program that accepts as input data representing codominant , single locus, diploid molecular markers (e.g., microsatellites ), applies to them the algorithm described in Lynch, M. & K. Ritland . 1999. Genetics 152:1753-1766 , and returns delta D and relatedness r estimates. Del rious can implement bootstrap and jackknife resampling procedures to provide confidence measures. Syntax templates for running analyses are contained in a notebook distributed with del rious . Del rious uses Mathematica (Wolfram Research, Inc. 2000) as a software platform and can be run under Linux, Macintosh, Microsoft Windows, or Unix operating systems.
http://www.zoo.utoronto.ca/stone/DELRIOUS/delrious.htm
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Tufto, J., S. Engen, and K. Hindar, 1996. Inferring patterns of migration from gene frequencies under equilibrium conditions. Genetics 144:1911-1921.
Tufto, J., A. F. Raybould, K. Hindar, and S. Engen, 1998. Analysis of genetic structure and dispersal patterns in a population of sea beet. Genetics in press.
http://www.ed.ac.uk/~jarlet/migration/ 25-Nov-99
S-Plus software required
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Valière, N. 2003. GIMLET : a computer program for analysing genetic individual identification data. Mol. Ecol. Notes 2: 377-379.
Laboratoire de Biométrie et de Biologie Evolutive, Université de Lyons, France
http://pbil.univ-lyon1.fr/software/Gimlet/gimlet%20frame1.html 18-Nov-04
Gimlet v. 1.3.2 software addresses issues in individual identification (e.g., forensic matching) where errors may result from low-quality DNA (e.g., from hair, feces). Among its abilities are: estimating error rates, false alleles and allelic dropout , finding matches, estimating kinship and providing several basic measures of genetic variability.
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Vekemans, X.. T. Beauwens, M. Lemaire, and I. Roldan-Ruiz. 2002. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol. Ecol. 11: 139-151.
Laboratoire de Génétique et d’Ecologie Végétales, Université de Libre de Bruxelles, Belgium
http://www.ulb.ac.be/sciences/lagev/aflp-surv.html 16-Jun-05
AFLP-Surveyt v. 1.0 AFLP-SURV estimates genetic diversity and population genetic structure from population samples analysed with AFLP or RAPD methods and computes genetic distance matrices between populations (Nei’s distance and 1-r measure based as developed or modified by Lynch and Milligan 1994). The program starts by estimating allelic frequencies at each marker locus in each population assuming they are dominant and have only two alleles (a dominant marker allele coding for the presence of a band at a given position, and a recessive null allele coding for the absence of the band). Relies heavily on methods developed in Lynch and Milligan (1994).
Lynch, M. and B.G. Milligan 1994. Analysis of population genetic structure with RAPD markers. Mol Ecol. 3: 91-99. * Indiana http://www.bio.indiana.edu/facultyresearch/faculty/Lynch.html
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Wilson, I.J., and D.J. Balding. 1998. Genealogical inference from microsatellite data. Genetics 150: 499-510.
http://www.maths.abdn.ac.uk/~ijw/ downloads/download.htm
Micsat Runs in C but has Windows executable 20-Oct-02 √
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Notes and scraps….
/mac/development/source/macstarterpascal1.0.cpt.hqx
168 12/19/93 BinHex4.0,Compact1.51
A simple application shell for THINK Pascal. Uses a window class
to provide basic window behavior: dragging, changing size,
zooming, closing and vertical and horizontal scroll bars. Detailed
knowledge of the THINK Class Library not required.
A source for computer software on the following topics: genetic linkage analysis, marker mapping, linkage disequilibrium mapping, and pedigree drawing.
http://www.nslij-genetics.org/soft/
Check on the following
Sequence Navigator
Mac seq.app
PRIMER!
http://www.math.yorku.ca/SCS/Demos/power/
will do sample size analysis for you simply and quickly. This will give you an idea of the sample size needed to detect differences at an error level that you choose. You have to set the parameters, for instance, if you want to detect a difference of 0.8 (the effect size) between two populations at some error level (say, 0.05), the program tells you that you will need to sample X number of individuals.
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Installing Structure 2.2 on Mac OSX.
1. Open a Terminal (UNIX interface) shell:
a. Find and open Terminal.app
b. Click “New shell” in the “File” menu
2. After the default prompt (something like “mcdg4-2:~ mcd$”), type (or better, paste) the full, path name for where the Structure program is housed. Note that UNIX does not allow spaces and certain other characters in folder (directory) names, and will give an error message saying that file or directory does not exist if you use sloppy folder-naming techniques. On my Intel Powerbook the path name is
“/Applications/ScienceApps/GeneticsPrograms/Structure222/structure”
3. Save the “new shell” as something like “StructureTerminalStarter”.
4. Keep that shell in the same folder that has the Structure 2.2 app.
5. Create aliases for the shell and put them wherever you actually want to start using Structure 2.2.
6. So far, I can’t seem to get the Mac version to run jobs (k = 1,2,3,….) or even to allow me to go back to an existing project (both of which work on the Windows version). That means it’s much less convenient, forcing me to run jobs one setup at a time….
The input file (since the manual is impenetrable) for AFLP data:
Line 1: list of n Loci
Line 2: list of n zeros
Lines 3 & 4 (duplicates): first “data lines”
Optional ID; optional population number; Extra column for Ord 1-166 with 5 digits missing for the 5 longnose suckers;
Population number codes: 1=B; 2=BF; 3=BW; 4=F; 5=FW; 6=W; 7=WS (Laramie River) then 1 for fragment present, 0 for fragment absent
101 103 105 106 108 113 114
0 0 0 0 0 0 0
20 UA2_2n AB1_E1M2_01_A01 1 0 0 0 1 0 0
20 UA2_2n AB1_E1M2_01_A01 1 0 0 0 1 0 0
24 MK_Cow AB13_E1M2_01_E02 0 0 0 0 0 0 0
24 MK_Cow AB13_E1M2_01_E02 0 0 0 0 0 0 0
23 MKWyeth AB14_E1M2_01_F02 1 0 1 0 0 0 1
23 MKWyeth AB14_E1M2_01_F02 1 0 1 0 0 0 1
* Thanks to Amy Blair of CSU for this tip
1.RNA draw 1.1 b
简介：RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
RNA draw 1.1b2 RNA二级结构分析软件,对RNA一级序列进行二级结构分析作图,最有意思的是大部分功能集中在鼠标右键。
下载地址：http://www.ibioo.com/soft/biosoft/20070806/1664.html
2.RNAstructure 4.5
简介：Unix平台软件mfold的for Windows版本，输入或载入RNA的一级序列,根据最小自由能原理,依据一定算法,预测出其二级结构图，非常出色的一个程序。
下载地址：http://www.ibioo.com/soft/biosoft/20070806/1665.html
3.Vienna RNA Package 1.64
简介：维也纳大学RNA二级结构预测与比较软件包。在windows下运行需要模拟linux环境的Cygwin。作者同时提供C语言源文件，感兴趣的人可以自行在WINDOWS下编译。
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