SMS: Smart Model Selection in PhyML
SMS (Smart Model Selection) automatically selects the best-fitting evolutionary model for an alignment of DNA or protein sequences. It compares substitution models using the AIC or BIC statistical criteria to support phylogenetic tree reconstruction with PhyML.
SMS: Smart Model Selection in PhyML online execution
Other tools
WAVES
Warning : This application is no longer maintained and out of date. If you’re interested in, just have a look to MYST Summary WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways:…
EPIK: Precise and scalable evolutionary…
EPIK is a program dedicated to « Phylogenetic Placement » (PP) of metagenomic or metabarcoding reads on a reference tree. It is similar in spirit and technically the successor of RAPPAS (Linard et al. 2020). EPIK achieves identical or slightly better accuracy than RAPPAS and outperforms it in speed and flexibility. In many aspects the documentation of RAPPAS…
PEWO: a collection of workflows…
Introduction and context In the Bioinformatics team of the LIRMM (CNRS & Univ. Montpellier), we develop a series of tools for metagenomics / metabarcoding analysis. Our tools exploit phylo-k-mers (which are k-mers combined with phylogenetic information) computed for an input set of reference sequences and their phylogeny. The phylo-k-mers are computed and indexed with IPK,…