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CodonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE).

Publication: CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

Authors: Manuel Gil, Marcelo Serrano Zanetti, Stefan Zoller and Maria Anisimova

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Artificial Life Framework (ALF), which aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation.

Publication: ALF—A Simulation Framework for Genome Evolution

Authors: Daniel A. Dalquen, Maria Anisimova,Gaston H. Gonnet and Christophe Dessimoz

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ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. This is achieved by incorporating a graph-based sequence representation as in POA and combines it with the advantages of the phylogeny-aware algorithm in Prank.

Publication: Graph-based modeling of tandem repeats improves global multiple sequence alignment

Authors: Adam M. Szalkowski, Maria Anisimova

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PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains:
– the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0)
– nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as 'templates'...

Publication: PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources

Authors: Slavica Dimitrieva, Maria Anisimova

Publication: Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

Authors: Slavica Dimitrieva, Maria Anisimova

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