Tools and Software

we recommend to download and install the with an asterisk* marked tools and files on your own laptop if possible - however, we will also provide a laptop for each student with most tools already installed

PHYLOGENETIC SOFTWARE

MRBAYES* - BAYESIAN INFERENCE OF PHYLOGENY

  • MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. 

RAXML* - RANDOMIZED AXELERATED MAXIMUM LIKELIHOOD

  • Tool for fast Maximum-likelihood based phylogenetic inference.

RAXMLGUI*

  • A graphical front-end  for RAxML

MEGA* - MOLECULAR EVOLUTIONARY GENETICS ANALYSIS

  • MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.  

PHYML 3.0

  • PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches

JMODELTEST*

  • jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies.

SEAVIEW*

  • Multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny

FIGTREE*

  • FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.

MAFFT

  • Multiple alignment program for amino acid or nucleotide sequences.

MUSCLE - POPULAR MULTIPLE ALIGNMENT SOFTWARE

  • MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds.

ARB PROJECT

ARB 

  • The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

ARB SILVA

  • A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

NEXT-GEN ANALYSIS

QIIME

  • QIIME (canonically pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics.

QIIME VIRTUAL BOX* & GREENGENES/SILVA DATABASE FOR QIIME*

SILVANGS

  • SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download.

MOTHUR

  • This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Mothur is currently the most cited bioinformatics tool for analyzing 16S rRNA gene sequences.

ADDITIONAL SOFTWARE - TOOLS - PACKAGES

SINA ALIGNMENT SERVICE

  • SINA will align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool.

R PROJECT & RSTUDIO (GUI)

  • R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.

PICANTE & VEGAN R-PACKAGES

  • The Picante package provides tools for Phylocom integration, community analyses, null-models, traits and evolution in R. The package includes functions for analyzing the phylogenetic and trait diversity of ecological communities, comparative analyses, and the display and manipulation of phenotypic and phylogenetic data.
  • VEGAN: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

PHYLOSEQ R-PACKAGE

  • The phyloseq package is a tool to import, store, analyze, and graphically display complex phylogenetic sequencing data that has already been clustered into Operational Taxonomic Units (OTUs), especially when there is associated sample data, phylogenetic tree, and/or taxonomic assignment of the OTUs.

BIOCONDUCTOR

  • Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.
  • The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.

GALAXY

  • Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

Course Data