https://heidi.chnebu.ch/ 2026-09-01T08:22:15+00:00 https://heidi.chnebu.ch/ https://heidi.chnebu.ch/lib/tpl/dokuwiki/images/favicon.ico text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=01.05.08&rev=1216726264&do=diff e-mail: 01.05.08 Hi: phyloXML version 1.00 has just been released. See: <http://www.phyloxml.org/> Thank you, text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=03.03.2008&rev=1216726264&do=diff meeting at 30.03.08 * data format: * study Geneious: what is it, what use it has (e-mail: Betreff: Evolution of Geneious is a success for bioinformatics worldwide|Biomatters: <http://www.biomatters.com/default,505,evolution_of_geneious_is_a_success_for_bioinformatics_worldwide.sm>) * HGDP (Human Genome Diversity Project): what format they have in the database, what format the extracted data have, text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=06.06.2008&rev=1216726264&do=diff meeting at 06.06.08 * additional converter formats to integrate: * BAPS * BayesAss/ Immanc * Batwing * FDist2, Lea, MSVar * MSA * GDA text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=09.06.08&rev=1216726264&do=diff e-mail: 09.06.08 Hi Heidi, please have a look at the following paper and program... <http://www.blackwell-synergy.com/links/doi/10.1111/j.1471-8286.2007.02036.x> It would be worth looking at... cheers laurent Program Create: <http://www.lsc.usgs.gov/CAFL/Ecology/Software.html> text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=10.02.08&rev=1216726264&do=diff e-mail: 10.02.08 Dear Howard, Howard Cann wrote: " Dear Laurent, Until now, the HGDP-CEPH diversity panel database has stored and displayed marker genotypes generated on the panel population samples. It is time that we receive sequences from panel users who are text/html 2008-07-22T13:31:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=12.02.2008&rev=1216726264&do=diff meeting at 12.02.08 * data format: * put in some further information: like linguistic family, etc. (see e-mail) * define if the data are like in Arlequin (diploid/haploid, aligned) or if there are several sequences of the same loci (not aligned) * display the data with XSLT. Is it possible to align it there? text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=14.03.2008&rev=1216726265&do=diff meeting at 14.03.08 * Arlequin output changes to XML: * root tag: Arlequin * Title: title * Data (PRE): data * how to jump to specific places in XML (like in HTML)? text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=14.12.2007&rev=1216726265&do=diff meeting at 14.12.07 * design of a new data format to store population genetics data: * XML or XML like * not to complex that you can have a look on your data in the text format * e.g.: * header: Name, Population, number of loci, history of loci (IDs), (loci information), no of individuals/sequences, interleaved data, text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=17.03.2008&rev=1216726265&do=diff meeting at 17.03.08 * file format: * different small changes * converter: * make a list of variables with the tag names at the beginnig, so that the tag names can be changed once at a central place if needed text/html 2008-10-20T15:58:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=20.10.2008&rev=1224511084&do=diff meeting at 20.10.08 last R-lequin changes * save pictures as .pdf * integrate pictures directly into the XML file (without buttons) * make attributes which sign if a graphic is available or not writing * general Introduction * PGD Spider text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=21.01.2008&rev=1216726265&do=diff meeting at 21.01.08 * Arlequin output change: make it together with Laurent at end of February/ begin of March * file format: * look at the different kind of blocks in NEXUS files * look at the different existing data types * DNA data: different sequences of the same loci (more than 2) text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=21.05.08&rev=1216726265&do=diff e-mail: 21.05.08 Morge Heidi, Hier noch ein R-Script mit einem Converter von AFLPDat zu dem Selection Programm von Matthieu. Gruss Tinu R-Script: convert_aflp<-function(input,output) { data=read.table(input,header=T) outfile=output nb_loci=ncol(data)-2 pops_names=levels(data[,2]) nb_pops=length(pops_names) cat("[loci]=",nb_loci,"\n\n",file=outfile) cat("[populations]=",nb_pops,"\n\n",file=outfile,append=T) for (pop in 1:nb_pops) { cur_pop=data[data[,2]==pops_names[pop],] n… text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=21.11.2007&rev=1216726265&do=diff meeting at 21.11.07 * Summary (review) of the different population genetics programs: * data type handled by the program (DNA, microsat,...) * haploid, diploid or polyploid data * How populations are defined * Problems/adventages * text/html 2008-07-23T21:36:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=23.07.2008&rev=1216841807&do=diff meeting at 23.07.08 * end of the master: final version at the end of november or till christmas * organize a copy of the tracking form (Susanne Maurer) text/html 2008-09-23T14:54:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=allelic_size_range&rev=1222174485&do=diff Allelic size range barplot * file: bar_AllelicSizeRang.r * documentation page: 3 code: read.table("D:/Heidi/Master/R_Daten/AllelicSizeRange/AllelicSizeRange_mic.txt", skip=4, row.names=1, fill=TRUE )-> Data Data nrow(Data) -> a ncol(Data) -> b Data2 <- as.matrix.data.frame(Data) Data3 <- Data2[1:(a-2),1:(b-3)] Data3 barplot(Data3, beside=TRUE, legend.text=TRUE, main="Allelic size range at different loci", xlab="Populations", ylab="Allelic size", … text/html 2011-07-07T11:16:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=arlequin&rev=1310030214&do=diff Arlequin Arlequin manual Arlequin ver 3.5 (released 24 February 2010) The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. text/html 2013-02-20T13:24:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=baps&rev=1361363074&do=diff BAPS BAPS manual Version 5.4 (29.04.2010) A program for Bayesian inference of the genetic structure in a population. Assigns individuals to genetic clusters by either considering them as immigrants (mixture analysis) or ad descendants from immigrants (admixture analysis). text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=batwing&rev=1216726265&do=diff BATWING Batwing documentation (2003) BATWING is a program written in C for the analysis of population genetic data. BATWING reads in multi-locus haplotype data, and model and prior distribution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also ge… text/html 2008-09-10T13:26:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=convert&rev=1221045977&do=diff CONVERT CONVERT version 1.31 (March 2005) CONVERT is a user-friendly, 32-bit Windows program that facilitates ready transfer of co-dominant, diploid genotypic data amongst commonly used population genetic software packages. Program information * Windows 95/98/NT/2000/XP text/html 2009-03-02T14:05:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=data_format&rev=1235999141&do=diff population genetics data format I will investigate the possibility to develop a new population genetics data format, which should facilitate the transfer of data among several population genetic software packages. data formats * Arlequin * GENEPOP * IM * text/html 2008-08-14T11:28:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=dnasp&rev=1218706098&do=diff DnaSP DnaSP Version 4.10.9 (September 13, 2006) DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several t… text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=expected_observed_haplotype&rev=1216726265&do=diff expected/observed haplotype barplot * file: bar2_HaplotypeFreq.r * document page: 6 code: read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ObsHaplotypeFreq_mt.txt”, skip=5, row.names=1, fill=TRUE )-> Observed nrow(Observed) -> rObs ncol(Observed) -> cObs newObserved <- Observed[1:(rObs-1),1:(cObs-1)] read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ExpHaplotypeFreq_mt.txt", skip=6, row.names=1, fill=TRUE) -> Expected nrow(Expected) -> rE… text/html 2008-07-22T13:31:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=fasta&rev=1216726265&do=diff FASTA wikipedia: FASTA format NCBI's FASTA format description FASTA format is a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. text/html 2011-09-19T16:19:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=fastq&rev=1316441981&do=diff FASTQ wikipedia: FASTQ format <http://nar.oxfordjournals.org/content/early/2009/12/16/nar.gkp1137.full> FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de fa… text/html 2011-06-10T11:23:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=fdist2&rev=1307697796&do=diff FDist2 (datacal) FDist2 [documentation] A program to detect loci that might be under selection in samples from structured populations. Program information * Linux * DOS Data type handled * Microsat * DNA * Standard (multi-allelic marker) Input Files fdist2 - this is the simulation program: text/html 2008-10-30T09:18:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=formatomatic&rev=1225354730&do=diff Formatomatic Formatomatic Current version 0.8.1 (released 14 May 2008) Formatomatic creates infiles for several population genetic analysis programs Program information * JRE (Java Runtime Environment) 1.6.0 has to be installed * Windows * MacOS text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=fst_matrix&rev=1216726266&do=diff Fst Matrix * file: matrix_FstMatrix.r * document page: 2 code: read.table("D:/Heidi/Master/R_Daten/FstMatrix/DistanceMatrix_mic.txt", header=TRUE, skip=1 ,row.names=1, fill=TRUE ) -> Data as.matrix.data.frame(Data) -> Matrix Matrix a <- ncol(Matrix) b <- nrow(Matrix) x <- c(1:a) y <- c(1:b) library(fields) ColorRamp <- rgb( seq(1,0,length=256), # Red seq(1,0,length=256), # Green seq(1,1,length=256)) # Blue image.plot(x,y,M… text/html 2010-04-27T15:40:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=fstat&rev=1272375612&do=diff FSTAT FSTAT version 2.9.3.2 (Feb. 2002) FSTAT estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods. Jackknife and Bootstrap confidence intervals are also provided. The windows version also estimates statistics developed for the stepwise mutation model (Rst and the like) text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=full_matrix&rev=1216726266&do=diff read full matrix data * file: read_tag-fullMatrix.r * document page: 38 code: #----open XML package----------------------------------------------------------- library(XML) #----read data between an XML tag----------------------------------------------- filename = "D:/Heidi/Master/R_Daten/XML/XML_with_inserted_data.xml" tag = "//pairwise_differences" doc = xmlTreeParse(filename, useInternal = TRUE) ch = getNodeSet(doc, tag) subDoc = xmlDoc(ch[[1]]) tagData <- xpathApply(subDoc, tag, x… text/html 2011-07-13T16:54:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=gda&rev=1310568865&do=diff GDA GDA [documentation] Version 1.1 (7 January 2002) Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics. Program information * Windows * Mac OS 10.2.8 and 10.3 (Jaguar and Panther) text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=genbank&rev=1216726266&do=diff GenBank GenBank format example: LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSION U49845 VERSION U49845.1 GI:1293613 KEYWORDS . SOURCE Saccharomyces cerevisiae (baker's yeast) ORGANISM Saccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomyce… text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=geneious&rev=1216726266&do=diff geneious geneious manual Geneious Version 3.5 (25 October 2007) Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. text/html 2011-05-31T11:38:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=geneland&rev=1306834699&do=diff Geneland Geneland manual Geneland (12. April 2011) Geneland is a computer program whose main goal is to process individual multilocus genetic data to detect population structure, i.e sub-populations at (or close to) Hardy-Weinberg and linkage equilibrium. Although the concept of population refers here to genetic structure only, it is often realistic to assume that populations are spatially organised. Toward this aim, Geneland is based on a spatially explicit model that can make use of bo… text/html 2011-07-07T11:29:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=genepop&rev=1310030978&do=diff GENEPOP GENEPOP documentation GENEPOP input file Genepop 4.1 (24.03.2011) It computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; It computes estimates of F-statistics, null allele frequencies, allele sizebased statistics for microsatellites, etc., and of number of immigrants by Barton & Slatkin's 1986 private allele method; text/html 2011-03-07T16:54:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=general_commands&rev=1299513290&do=diff general commands * install.packages(“packageName”): download and install a package --> start R as following: Rgui.exe --internet2 * help(package=XML): information about the package XML * str(a): display the structure of a object * table(x) text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=genetix&rev=1216726266&do=diff GENETIX GENETIX Version 4.05 (05.05.2004) This set of programs computes several basic parameters of population genetics such as Nei's D and H, Wright's F-statistics (the Weir-Cockerham's and Robertson-Hill's estimators), and linkage disequilibrium D according to Black & Krafsur. For each of them, the distribution of the parameter values under the null hypothesis (for instance Hardy-Weinberg equilibrium for Fstats) is generated by the appropriate resampling scheme of the relevant objects (e.… text/html 2011-07-07T11:32:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=geste_bayescan&rev=1310031167&do=diff GESTE/ BayeScan BayeScan GESTE BayeScan (version 2.01): This program identifies candidate loci under natural selection. It's applicable to both, dominant and codominant data. GESTE (version 2.0): (GEnetic STructure inference based on genetic and Environmental data) is a Bayesian method to evaluate the effect that biotic and abiotic environmental factors (geographic distance, language, temperature, altitude, local population sizes, etc.) have on the genetic structure of populations. … text/html 2008-09-23T09:44:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=half_matrix&rev=1222155858&do=diff read half matrix data * file: read_tag-halfMatrix.r * document page: 37 code: #----open XML package------------------------------------------------- library(XML) #----read data between an XML tag------------------------------------- filename = "D:/Heidi/Master/R_Daten/XML/PairwiseFst_XML2.xml" tag = "//Fst" doc = xmlTreeParse(filename, useInternal = TRUE) ch = getNodeSet(doc, tag) subDoc = xmlDoc(ch[[1]]) tagData <- xpathApply(subDoc, tag, xmlValue) free(subDoc) #----convert string… text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=haplotype_distance_between_within_populations_and_groups&rev=1216726266&do=diff haplotype distance between/within populations and groups * file: matrix_multiplePlots.r * document page: 25 code: #----read data------------------------------------------------------------------ #----read haplotype list---- Data <- read.table("D:/Heidi/Master/R_Daten/HaplotypeDistance/ListHaplotype_betweenPop.txt", skip=1) Row <- nrow(Data) Columns <- Row #----read data row by row:---- x <- 0 n <- 1 DistanceMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/HaplotypeDistance/ … text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=haplotype_distance_between_within_two_populations&rev=1216726267&do=diff haplotype distance between/within two populations * file: matrix_HapDistance_between-within.r * document page: 11 code: #----read haplotype list---- Data <- read.table("D:/Heidi/Master/R_Daten/HaplotypeDistance/ListHaplotype_betweenBsp.txt",skip=1) Row <- nrow(Data) Columns <- Row #----read data row by row:---- x <- 0 n <- 1 DistanceMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/HaplotypeDistance/HapDistanceMatrix_betweenBsp.txt, what=double(0), … text/html 2008-07-22T13:31:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=haplotype_distance&rev=1216726266&do=diff haplotype distance * file: matrix_HapDistanceMatrix.r * document page: 5 code: Data <- read.table("D:/Heidi/Master/R_Daten/HaplotypeDistance/HapDistanceMatrix_mt.txt" , skip=1) Columns <- ncol(Data ) + 1 Row <- nrow(Data) x <- 3 n <- 1 DistanceMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/HaplotypeDistance/HapDistanceMatrix_mt.txt", what=double(0), skip=x, nlines=1, nmax=n), row.names=1) DistanceMatrix <- cbind(DistanceMatrix, matrix(NA, ncol=(Co… text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=haplotype_frequencies_in_population&rev=1216726267&do=diff Haplotype frequencies in population * file: lines_HaplotypeFreqMultiple.r * document page: 29 code: #----read data------------------------------------------------------------------ Names <- scan("D:/Heidi/Master/R_Daten/SummaryStatistics/haplotype_frequ.txt", what="list", skip=5, nlines=1) Data <- read.table("D:/Heidi/Master/R_Daten/SummaryStatistics/haplotype_frequ.txt", skip=8) nRow <- nrow(Data) nCol <- ncol(Data) #----draw plot--------------------------------------… text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=hapmap&rev=1216726267&do=diff HapMap format * The header of Hapmap format files looks like: rs#SNPalleleschromposstrand genome_build centerprotLSID assayLSIDpanelLSIDQC_code followed by a list of sample identifiers. * a sample line of the hapmap format genotype file: rs169757 A/C Chr21 9928594 + ncbi_b35.1 broad urn:LSID:affymetrix.hapmap.org:Protocol:genotype_protocol_1:1 urn:LSID:affymetrix.hapmap.org:Assay:1612756:1 urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1 QC+ AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA A… text/html 2013-11-19T15:11:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=heidi_lischer&rev=1384870302&do=diff about me Name Lischer Prename Heidi Birthday 11.11.1985 e-mail heidi.lischer(at)iee.unibe.ch Adress (privat) Bergheim 6216 Mauensee Adress (CMPG) Room D305 Computational and Molecular Population Genetics Lab Institute of Ecology and Evolution text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=heterozygosity&rev=1216726267&do=diff heterozygosity * file: line_Heterozygosity.r * document page: 2 code: read.table("D:/Heidi/Master/R_Daten/Heterozygosity/heterocy_mt.txt")-> heterocy attach(heterocy) V1 -> Locus V2 -> het V3 -> mean V4 -> sd V5 -> total.het plot(Locus, het, type="l", xlab="Loci", ylab="heterozygosity", main="Heterozygosity") detach(heterocy) text/html 2011-07-07T11:34:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=hgdp-ceph&rev=1310031279&do=diff HGDP-CEPH <http://www.cephb.fr/hgdp-cephdb/> The HGDP-CEPH Diversity Panel Database is designed to receive and store polymorphic marker genotypes generated by users of the DNAs of the HGDP-CEPH Diversity Panel. The data are accessible publically via a web interface (database V3.0 only) and/or as flat files (V3.0; Supplements 1 and 2). These panel DNAs presently are produced from 1064 lymphoblastoid cell lines (LCLs) representing some 1064 individuals sampled from 51 populations throughout th… text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=hickory&rev=1216726267&do=diff HICKORY HICKORY documentation version 1.1 Software for analysis of geographic structure in genetic data. 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). text/html 2011-07-14T14:26:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=im&rev=1310646384&do=diff IM IM documentation updated 17.12.2009 IM is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. Large numbers of loci can be studied simultaneously, and different mutation models can be used. IM estimates the divergence time and the migrations having occurred in the ancestry of two populations, which might have grown exponentially since split. Important limitations of the basic model are that it cannot … text/html 2013-05-03T10:34:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=ima2&rev=1367570054&do=diff IMa2 IMa2 <http://lifesci.rutgers.edu/~heylab/ProgramsandData/Programs/IMa2/Using_IMa2_8_24_2011.pdf> updated 26.08.2011 The program implements a method for generating posterior probabilities for complex demographic population genetic models. IMa2 works similarly to the older IMa program, with some important additions. IMa2 can handle data and implement a model for multiple populations (for numbers of sampled populations between one and ten) – not just two populations (as was the case wit… text/html 2011-07-07T12:59:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=immanc&rev=1310036379&do=diff Immanc (BayesAss) <http://www.rannala.org/?page_id=13/ BayesAss> documentation Immanc: Version 5.0 (8 Oct 1998) Detecting Immigrants Using Multilocus Genotypes. BayesAss+: Version 1.3 (Date 4 May 2005) Bayesian Estimation of Recent Migration Rates Using Multilocus Genotypes. BayesAss: Version 2.0 (not released yet) text/html 2009-03-09T20:26:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=kml&rev=1236626796&do=diff KML KML version 2.2 KML is a file format used to display geographic data in an Earth browser such as Google Earth, Google Maps, and Google Maps for mobile. KML uses a tag-based structure with nested elements and attributes and is based on the XML standard. text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=lamarc&rev=1216726267&do=diff LAMARC LAMARC version 2.1.2b Lamarc is a program for doing Likelihood Analysis with Metropolis Algorithm using Random Coalescence. Lamarc estimates effective population sizes, population exponential growth rates, a recombination rate, and past migration rates for one to n populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. text/html 2024-02-01T16:26:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=main_page&rev=1706801208&do=diff Master thesis - Population genetics data acquisition and visualization Master of Science (MSc) in Ecology and Evolution, Institute of Ecology and Evolution (IEE), Division of Population Genetics (CMPG) subject * R-lequin * population genetics data format * PGD * data converter: text/html 2008-07-22T13:31:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=meeting_vom_21.11.2007&rev=1216726267&do=diff Mastererweiterung converter: * Which data type it handle (DNA, Microsat,...) * diploid, haploid or polyploid data * How populations are defined * Problems/Advantages * Zusammenfassung machen * wie kann man diese in eine gemeinsame Sprache umwandeln text/html 2008-10-20T15:42:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=meetings&rev=1224510131&do=diff Master thesis meetings * 21.11.2007: converter: data formats * 14.12.2007: data formats/universal format, R-lequin: Arlequin output * 21.01.2008: file format * 12.02.2008: file format * 03.03.2008: file format/ converter * 14.03.2008: Arlequin output * 17.03.2008: file format * ... * 06.06.2008: converter * text/html 2011-07-07T11:50:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=mega&rev=1310032219&do=diff MEGA MEGA documentation Version 5 (Aril 24, 2011) MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. text/html 2011-07-14T15:02:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=migrate&rev=1310648525&do=diff MIGRATE MIGRATE documentation Version 3.2.6 (13. October 2010) Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy. The estimates of the parameter values are achieved by either a Maximum likelihood (ML-approach or Bayesian inference (BI)). text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=mismatch_distribution&rev=1216726268&do=diff mismatch distribution * file: lines_Mismatch.r * document page: 1 code: read.table("D:/Heidi/Master/R_Daten/Mismatch/Mismatch_mt4.txt")-> mismatch4 mismatch4 attach(mismatch4) V1 -> Diff V2 -> Observed V3 -> Low.bound V4 -> Up.bound V5 -> ModelFreq. max(Up.bound) -> max1 plot(Diff, Observed, type="l", ylim=c(0,max1), xlab="differences", ylab="number", main="Mismatch distribution") lines(Diff, Low.bound, lty=2) lines(Diff, Up.bound, lty=2) legend("t… text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=molecular_diversity_indexes&rev=1216726268&do=diff Molecular diversity indexes * file: lines_MolecDiversityIndexes.r * document page: 30 code: #----read data------------------------------------------------------------------ Names <- scan("D:/Heidi/Master/R_Daten/SummaryStatistics/molec_diversity_indexes.txt", what="list", skip=6, nlines=1) Data <- read.table("D:/Heidi/Master/R_Daten/SummaryStatistics/molec_diversity_indexes.txt", skip=8, row.names=1) Data <- as.matrix(Data[1:(length(Data)-2)]) #----… text/html 2008-07-30T12:07:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=msa&rev=1217412457&do=diff MSA MSA Version 4.05 The MSA software tool was designed to handle large microsatellite data sets. Microsatellite analyzer calculates the standard suit of descriptive statistics and provides input files for other software packages. Program information text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=msvar&rev=1216726268&do=diff MSVar MSVar [documentation] Version 0.4.1.b (7 April 1999) This program is designed to help the user explore the most probable demographic and genealogical histories consistent with a sample of chromosomes typed at one or more loci. It relies on Markov Chain Monte Carlo (MCMC) simulation. text/html 2008-08-14T14:12:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=navigation&rev=1218715930&do=diff * main page * R-lequin * population genetics data format * PGD * data converter: PGDSpider * meetings * syntax text/html 2011-06-03T17:20:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=newhybrids&rev=1307114447&do=diff NewHybrids NewHybrids manual NewHybrids version 1.1 beta (7. April 2003) NewHybrids is a program for computing the posterior distribution that individuals in a sample fall into different hybrid categories. Program information * Mac * Windows Data type handled text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=nexus&rev=1216726268&do=diff NEXUS [NEXUS]: Description in Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46:590-621. NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. text/html 2008-11-24T09:55:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=old_versions&rev=1227516905&do=diff PGD: old versions * root element: <PGD> * microsat data are number of repeats * nucleotid data: just one loci in one tag (popLoci/ indLoci)! (If more than one loci: repeat the whole ind tag for every loci) * stylesheet: 1. version: text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=paml&rev=1216726268&do=diff PAML - Phylogenetic Analysis by Maximum Likelihood PAML documentation Version 4 (July 2007) PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. text/html 2011-06-08T09:42:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=ped&rev=1307518961&do=diff PED PED PED The “ped” file format refers to the widely-used format for linkage pedigree data and used as input for the program PLINK. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. text/html 2009-01-17T10:43:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_aligned_diffdatatypes&rev=1232185422&do=diff PGD file example Aligned data with different data types: <?xml version="1.0" encoding="iso-8859-1"?> <?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?> <PGD> <header title="Fake HLA data"> <numPop> 2 </numPop> <ploidy> 1 </ploidy> <aligned> yes </aligned> <missing> ? </missing> <gap> - </gap> <gameticPhase> known </gameticPhase> </header> <dataDescription> <numLoci> 2 </numLoci> <dataType> mixed </dataType> <locus id="loci one"> … text/html 2009-01-17T10:42:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_aligned&rev=1232185357&do=diff PGD file examples aligned data: <?xml version="1.0" encoding="iso-8859-1"?> <?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?> <PGD> <header title="Fake HLA data"> <numPop> 4 </numPop> <ploidy> 2 </ploidy> <aligned> yes </aligned> <missing> ? </missing> <gap> - </gap> <gameticPhase> known </gameticPhase> </header> <dataDescription> <numLoci> 2 </numLoci> <dataType> Standard </dataType> <locus id="loci one"> <locusChromosome> 3… text/html 2011-10-11T15:51:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_diffdatatypes&rev=1318341093&do=diff PGD file example Data of two loci with different data types (Standard and DNA) from two diploid populations: <?xml version="1.0" encoding="iso-8859-1"?> <?xml-stylesheet type="text/xsl" href="stylesheet_data-format3.xsl"?> <PGD xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="PGD_schema.xsd"> <header title="Fake HLA data"> <numPop> 2 </numPop> <ploidy> 1 </ploidy> <missing> ? </missing> <gap> - </gap> <gameticPhase> known </gameti… text/html 2011-10-11T15:52:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_ngs&rev=1318341151&do=diff PGD file example NGS data of two loci from three haploid populations: <?xml version="1.0" encoding="iso-8859-1" ?> <?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?> <PGD xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="PGD_schema.xsd"> <header title="faked example data"> <organism> homo sapiens sapiens </organism> <numPop> 3 </numPop> <ploidy> 1 </ploidy> <missing> ? </missing> <gap> - </gap> </header> <dataDescripti… text/html 2012-05-07T09:11:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_spider_-_manual&rev=1336374703&do=diff PGDSpider Manual PGDSpider version 2.0.1.6 (May 2012) PGDSpider download PGDSpider - changelog PGDSpider program description Definition of PGD fileformat System requirements: PGDSpider is written in Java and therefore platform independent, but SUN Java 1.6 RE (or a newer version) has to be installed. Java6 RE can be downloaded under following link: text/html 2011-10-11T15:50:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_standard&rev=1318341035&do=diff PGD file examples Data of two loci with Standard data type from four diploid populations: <?xml version="1.0" encoding="iso-8859-1"?> <PGD xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="PGD_schema.xsd"> <header title="Fake HLA data"> <numPop> 4 </numPop> <ploidy> 2 </ploidy> <missing> ? </missing> <gap> - </gap> <gameticPhase> known </gameticPhase> </header> <dataDescription> <numLoci> 2 </numLoci> <dataType> Sta… text/html 2011-05-05T17:30:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd_unaligned_mixedreads&rev=1304609454&do=diff PGD file example Unaligned data with mixed number of reads: <?xml version="1.0" encoding="iso-8859-1" ?> <?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?> <PGD> <header title="faked example data"> <organism> homo sapiens sapiens </organism> <numPop> 3 </numPop> <ploidy> 1 </ploidy> <aligned> no </aligned> <missing> ? </missing> <gap> - </gap> </header> <dataDescription> <numLoci> 2 </numLoci> <dataType> DNA </dataType> <locus id="loci … text/html 2016-02-22T15:41:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgd&rev=1456152083&do=diff PGD - Population Genetics Data format Version 1.1 PGD (Population Genetics Data) is a file format designed to contain population genetics data. The aim of this format is to facilitate the transfer among several population genetics software packages. PGD plays an important role in the new data format converter PGDSpider. text/html 2016-02-22T15:39:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=pgdspider&rev=1456151941&do=diff PGDSpider PGDSpider version 2.0.6.0 (Juli 2014) PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly used to store and han… text/html 2011-07-07T12:49:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=phylip&rev=1310035762&do=diff PHYLIP PHYLIP Version 3.69 (September 2009) PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=population_assignment_test&rev=1216726268&do=diff Population assignment test * file: points_assignmentTest.r * document page: 24 code: #----read data-------------------------------------------------------------- sample1 <- read.table("D:/Heidi/Master/R_Daten/assignmentTest/sample1.txt", skip=3 ) sample2 <- read.table("D:/Heidi/Master/R_Daten/assignmentTest/sample2.txt", skip=3 ) sample1 <- as.matrix(sample1[2:3]) sample2 <- as.matrix(sample2[2:3]) min_x <- min(sample1[,1], sample2[,1]) min_y <- min(sample1[,2], sample2[… text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=population_average_pairwise_difference&rev=1216726268&do=diff Population average pairwise difference * file: matrix_PairwiseDifferences.r * document page: 33 code: #----read data------------------------------------------------------------------ Data <- read.table("D:/Heidi/Master/R_Daten/SummaryStatistics/pairwise_differences.txt", skip=10, row.names=1) DataMatrix <- as.matrix(Data) #----UnderMatrix---- n <- 2 x <- 1 UnderMatrix <- matrix(NA, ncol=ncol(DataMatrix), nrow=1) while(n<=nrow(DataMatrix)){ nextrow <- DataMatrix… text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=powermarker&rev=1216726268&do=diff PowerMarker PowerMarker manual Version 3.25 (released on 2/5/2006) PowerMarker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results. text/html 2009-01-17T10:55:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=r-lequin&rev=1232186138&do=diff R-lequin R-lequin is a collection of R functions to parse a XML output file of ARLEQUIN version 3.12. R-lequin extracts data and produces graphics. R is an ideal programming language for parsing XML files and for graphic creation because it provides a lot of graphical techniques and a XML package containing tools for parsing and generating XML within R. The graphics should help to get an impression and to interpret the results produced by ARLEQUIN. text/html 2008-07-22T13:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=read_data_between_xml_tags&rev=1216726268&do=diff read data between XML tags * file: Node auslesen_BspTabelle.r * document page: 19 code: #----open XML package------------------------------------------------- library(XML) #----read data between an XML tag------------------------------------- filename = "D:/Heidi/Master/R_Daten/XML/Beispiel.xml" tag = "//Fst" doc = xmlTreeParse(filename, useInternal = TRUE) ch = getNodeSet(doc, tag) subDoc = xmlDoc(ch[[1]]) tagData <- xpathApply(subDoc, tag, xmlValue) free(subDoc) #print(tagData, ind… text/html 2008-07-22T13:31:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=relative_fis_per_locus&rev=1216726269&do=diff relative Fis per locus * file: bar_FisLocusRelative.r * document page: 4 code: read.table("D:/Heidi/Master/R_Daten/Fis/FisLocus_mic.txt", skip=16, row.names=1, fill=TRUE , nrows=4, na.strings= "N.A.")-> Data Data #wandelt alle NA in 0 um: for(i in 1:ncol(Data)) if(is.numeric(Data[,i])) Data[is.na(Data[,i]), i] <- 0 Data nrow(Data) -> a ncol(Data) -> b Data2 <- as.matrix.data.frame(Data) barplot… text/html 2008-07-22T13:31:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=solexa&rev=1216726269&do=diff SOLEXA e-mail: Dear all, On Tue, 11 Dec 2007 11:33:35 +0100, Jean-Louis C. Blouin wrote: > To add in the technical ideas, would it be possible (in the excel > results) to have an indication of the overal quality of sequencing. I > know that we are dealing with hundred of sequences. But for example > having a (or couple) score saying that the substitution that is seen > in 20 out of 400 sequences was of xx score would be very usefull. I have now pretty much completed a first analysis of… text/html 2011-07-07T12:54:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=structure&rev=1310036080&do=diff STRUCTURE STRUCTURE documentation Version 2.3.3 (January 2010) The program structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. It includes inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. text/html 2008-07-22T13:31:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=table&rev=1216726269&do=diff read able data with names * file: read_tag-table(with names).r * document page: 39 code: #----open XML package----------------------------------------------------------- library(XML) #----read data between an XML tag----------------------------------------------- filename = "D:/Heidi/Master/R_Daten/XML/XML_with_inserted_data.xml" tag = "//theta" doc = xmlTreeParse(filename, useInternal = TRUE) ch = getNodeSet(doc, tag) subDoc = xmlDoc(ch[[1]]) tagData <- xpathApply(subDoc, tag, xmlVa… text/html 2008-07-22T13:31:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=tau&rev=1216726269&do=diff Divergence times allowing for unequal population sizes (tau) * file: matrix_tau.r * document page: 31 code: #----read data------------------------------------------------------------------ Data <- read.table("D:/Heidi/Master/R_Daten/SummaryStatistics/tau.txt", skip=5, fill=TRUE) Columns <- ncol(Data)+1 Row <- nrow(Data) x <- 6 n <- 2 #----read data line by line----------------------------------------------------- tauMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/SummaryStatistics… text/html 2008-07-22T13:31:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://heidi.chnebu.ch/doku.php?id=xml_presentation&rev=1216726269&do=diff XML presentation * [XML presentation] links tutorials * XML (german) * XML (englisch, w3schools) * XSLT * XPath * XSL-FO XML in R * functions of the XML package