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GCATemplates available: grace

AAF homepage

Use the module spider command to see the available versions of AAF:

 module spider AAF

AAF (alignment and assembly-free) is a free software package that reconstructs phylogeny from next-generation sequencing data without assembly and alignment.

It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.

If you are running aaf_distance.py with > 10 cores and the command is failing with a message like IndexError: list index out of range then use fewer cores such as -t 5