Phylogenomics with RAxML and FastTree

This tutorial demonstrates a RAxML(1) and FastTree(2) analysis on a multiple alignment in a BIONUMERICS database. 

(1): Alexandros Stamatakis. Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9):1312–1313, 2014. (2): Morgan N Price, Paramvir S Dehal, and Adam P Arkin. Fasttree 2–approximately maximumlikelihood trees for large alignments. PloS one, 5(3), 2010.

Sequences

Nucleic acid or amino acid sequences, from import and assembly over multiple alignment to annotation, SNP analysis, primer design and comparison of complete chromosomes.

Download PDF file: 
Download demonstration database: 
WGS_demo_database_for_Burkholderia_cepacia

Demonstration database containing data for a set of 38 Burkholderia cepacia complex isolates. This database uses publicly available genome assemblies imported from NCBI. wgMLST alleles were called using the assembly-based method.

Note that the downloaded database backup file (.bnbk) can be restored via the Restore database... functionality in the BIONUMERICS startup screen.