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AB3130xl Genetic Analyzer (Applied Biosystems)
96-well plate assembly
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 |
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).
| 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. | - |