SalzburgerLab Protocols

AB3130xl Genetic Analyzer

AB3130xl Genetic Analyzer (Applied Biosystems)

AB3130xl Genetic Analyzer

96-well plate assembly

Using the AB3130xl Sequencer

Sequence Analysis

Microsatellite Analysis



A comprehensive tutorial on how to use our database: database_tutorial.pdf

Excel sheet for import of data into database tables: database_import.xlsx
Very simplified database import sheet intended for field trips: database_import_fw.xls

SQL code for import of data from the above Excel sheet into database tables (use right-click and 'Save As'):

Table SQL code Add-on scripts
amplicon addToAmplicon.sql
digital_material addToDigital_material.sql
extraction addToExtraction.sql
field_trip addToField_trip.sql
landmark_file addToLandmark_file.sql
organism addToOrganism.sql depth_range_plotter.rb
organism2primer addToOrganism2primer.sql
primer addToPrimer.sql
primer2amplicon SQL code obsolete
reference addToReference.sql
sample addToSample.sql
specimen addToSpecimen.sql
specimen2specimen SQL code obsolete
station addToStation.sql google_earth_exporter.rb

Computer analyses

Complete tutorial on publishable phylogenies

This tutorial summarizes knowledge gained during the Workshop on Molecular Evolution 2009. The workflow includes sequence alignment using MAFFT, phylogenetic analyses using GARLI, RAxML, and MrBayes, and tree visualization with FigTree. The tutorial is in Keynote or PowerPoint format. PowerPoint may run less smooth than Keynote. Some explanations to the slides are given as notes below the slides (Keynote: View > Show Presenter Notes).

How to run software remotely on the server (evo-lutra)

Software we use and its availability on the server (evo-lutra)

Name Description Server
Codoncode Aligner Software for sequence assembly, contig editing, and mutation detection. -
4Peaks Free alternative for sequence editing. -
ClustalW Command line tool for multiple sequence alignments. +
Gblocks Selection of conserved blocks from multiple sequence alignments -
MAFFT Multiple Alignment using Fast Fourier Transform. -
Muscle Multiple alignment software for protein and nucleotide sequences. +
PAUP* Command line tools for inferring and interpreting phylogenetic trees. +
RAxML Worlds fastest maximum likelihood algorithm for phylogenetic inference. +
MrBayes Bayesian inference of phylogeny +
IM MCMCMC Implementation of the isolation with migration model. +
IMa MCMCMC Implementation of the isolation with migration model. +
Populations Yet another population genetic software. +
FigTree Fancy graphical viewer of phylogenetic trees. -
Genemapper Genotyping software package. -
Peak Scanner Free alternative for Genotyping. -
MSA Microsatellite analysis and flexible file format conversion. -
Arlequin An integrated software for population genetics data analysis. -
Structure Interpreting population structure from microsatellite data. +
Past Statistical analysis of morphometric data. -
TpsDig2 Digitizes landmarks and outlines for geometric morphometric analyses. -
TpsRelw Performes a relative warp analysis. -
Makefan6 Tool for drawing alignment “fans” at equal angular spacing on an image prior to digitization. -
R The language for statistical computing. +
LaTeX The real alternative to MS Word. -